2016-10-27  Gemma Guest  <gb10@sanger.ac.uk>
 Fix organisms window size when using suffix - BUG FIX
 src/belvuApp/belvuMain.cpp   | 10 ++++++++--
 src/belvuApp/belvuWindow.cpp | 16 +++++++++++-----
 2 files changed, 19 insertions(+), 7 deletions(-)

2016-10-26  Gemma Guest  <gb10@sanger.ac.uk>
 Fix organisms window size - BUG FIX
 src/belvuApp/belvu.cpp       | 6 ++++++
 src/belvuApp/belvuWindow.cpp | 5 ++++-
 src/belvuApp/belvu_.hpp      | 1 +
 3 files changed, 11 insertions(+), 1 deletion(-)

2016-10-26  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bug with duplicate organisms - BUG FIX
 src/belvuApp/belvu.cpp | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

2016-10-26  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bug parsing organism lines - BUG FIX
 src/belvuApp/belvu.cpp     | 13 ++++++++++---
 src/belvuApp/belvuMain.cpp | 14 +++++++-------
 2 files changed, 17 insertions(+), 10 deletions(-)

2016-09-26  zmap  <zmap@sanger.ac.uk>
 Merge branch 'release/4.44.0' into production
2016-09-23  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.43.0-13-g8e07 - Update RT and git commit reports
 src/ChangeLog                                  | 20 ++++++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 14 ++++++++++++--
 3 files changed, 33 insertions(+), 2 deletions(-)

2016-09-16  Gemma Guest  <gb10@sanger.ac.uk>
 Update release notes - DOC
 src/doc/User_doc/release_notes.html | 24 +++++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

2016-09-16  Gemma Guest  <gb10@sanger.ac.uk>
 Add environment and X11 to instructions - DOC
 src/INSTALL.VM    | 20 ++++++++++++++++++++
 src/INSTALL.linux | 25 +++++++++++++++++++++++++
 src/INSTALL.mac   | 31 +++++++++++++++++++++++++++++++
 src/README        |  4 ++++
 4 files changed, 80 insertions(+)

2016-09-13  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.43.0-10-g2cfb - Update RT and git commit reports
 src/ChangeLog                                  | 933 ++-----------------------
 src/build/release_docs/GIT_COMMITS.txt         |  15 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  14 +-
 3 files changed, 57 insertions(+), 905 deletions(-)

2016-08-11  Ed Griffiths  <edgrif@sanger.ac.uk>
 Move to c++11 standard. - BUILD
 src/Makefile.am.common | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-08-03  Gemma Guest  <gb10@sanger.ac.uk>
 Fix regression from 1e60e02 - REGRESSION FIX
 src/blixemApp/blxcontext.cpp | 2 +-
 src/blixemApp/detailview.cpp | 2 +-
 src/dotterApp/dotter.cpp     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

2016-08-02  Gemma Guest  <gb10@sanger.ac.uk>
 Fix problems with multiple groups - BUG FIX
 src/blixemApp/bigpicturegrid.cpp       |  6 ++--
 src/blixemApp/blxcontext.cpp           | 61 ++++++++++++++++++++++++++++++++--
 src/blixemApp/blxcontext.hpp           |  4 ++-
 src/blixemApp/blxwindow.cpp            |  4 +--
 src/blixemApp/detailviewtree.cpp       | 10 +++---
 src/blixemApp/exonview.cpp             |  6 ++--
 src/blixemApp/sequencecellrenderer.cpp |  2 +-
 7 files changed, 75 insertions(+), 18 deletions(-)

2016-07-28  Gemma Guest  <gb10@sanger.ac.uk>
 Minor fix to docs - DOC
 src/INSTALL.VM | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-07-28  Gemma Guest  <gb10@sanger.ac.uk>
 Add VirtualBox installation instructions - DOC
 src/INSTALL.VM | 159 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 src/README     |  50 ++++++++++--------
 2 files changed, 187 insertions(+), 22 deletions(-)

2016-07-22  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'production' into develop
2016-07-22  Gemma Guest  <gb10@sanger.ac.uk>
 Fix up last month's release notes - DOC
 src/doc/User_doc/release_notes.html | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

2016-07-22  zmap  <zmap@sanger.ac.uk>
 Merge branch 'release/4.43.0' into production
2016-07-21  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a problem with font width highlighting in belvu - BUG FIX
 src/belvuApp/belvuAlignment.cpp |  2 +-
 src/blixemApp/blxcontext.cpp    |  2 +-
 src/blixemApp/detailview.cpp    |  2 +-
 src/dotterApp/dotter.cpp        |  2 +-
 src/seqtoolsUtils/utilities.cpp | 34 +++++++++++++++++++++++++++-------
 src/seqtoolsUtils/utilities.hpp |  2 +-
 6 files changed, 32 insertions(+), 12 deletions(-)

2016-07-21  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-123-g99e0 - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

2016-07-19  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'release/4.43.0' into develop
2016-07-18  Gemma Guest  <gb10@sanger.ac.uk>
 Remove hack to hard-code -lX11 and -lm - BUILD
 src/belvuApp/Makefile.am  | 2 +-
 src/blixemApp/Makefile.am | 2 +-
 src/dotterApp/Makefile.am | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

2016-07-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-122-ge38c - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

2016-07-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-121-ga2cdc - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 3 ++-
 2 files changed, 8 insertions(+), 1 deletion(-)

2016-07-08  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-120-g943b - Update RT and git commit reports
 src/ChangeLog                                  | 5 +++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

2016-07-07  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-119-g08c2 - Update RT and git commit reports
 src/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

2016-07-07  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-118-ge73e - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2016-07-06  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-117-g6b78 - Update RT and git commit reports
 src/ChangeLog                                  | 24 ++++++++++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  2 --
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 25 insertions(+), 3 deletions(-)

2016-07-05  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'release/4.43.0' into develop
2016-07-05  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-111-g00f2 - Update RT and git commit reports
 src/ChangeLog | 7 +++++++
 1 file changed, 7 insertions(+)

2016-07-05  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-110-geacf0 - Update RT and git commit reports
 src/ChangeLog                                  | 10 ++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 12 insertions(+), 1 deletion(-)

2016-06-30  Ed Griffiths  <edgrif@sanger.ac.uk>
 Update to fixes etc. for this releaes. - DOC
 src/doc/User_doc/release_notes.html | 5 +++++
 1 file changed, 5 insertions(+)

2016-06-29  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-108-g8fb3b - Update RT and git commit reports
 src/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

2016-06-29  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-107-ga06d - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2016-06-29  Gemma Guest  <gb10@sanger.ac.uk>
 Logging - TRIVIAL
 src/autogen.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-06-29  Gemma Guest  <gb10@sanger.ac.uk>
 Logging - TRIVIAL
 src/autogen.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-06-29  Gemma Guest  <gb10@sanger.ac.uk>
 Logging - TRIVIAL
 src/autogen.sh | 1 +
 1 file changed, 1 insertion(+)

2016-06-27  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-106-ga491 - Update RT and git commit reports
 src/ChangeLog                                  | 11 +++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 13 insertions(+), 1 deletion(-)

2016-06-27  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.43.0' into develop
2016-06-27  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bug finding data type - REGRESSION FIX
 src/seqtoolsUtils/blxGff3Parser.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2016-06-24  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-104-gb8ea - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

2016-06-22  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-103-g89545 - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2016-06-21  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-102-gc940 - Update RT and git commit reports
 src/ChangeLog                                  | 185 +++++++++++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  10 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  12 +-
 3 files changed, 203 insertions(+), 4 deletions(-)

2016-06-20  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/groups' into develop
2016-06-20  Gemma Guest  <gb10@sanger.ac.uk>
 Add groups list to scrolled window - WIP
 src/blixemApp/blxwindow.cpp | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

2016-06-20  Gemma Guest  <gb10@sanger.ac.uk>
 Add option to hide a source - WIP
 src/blixemApp/blxcontext.cpp | 47 ++++++++++++++++++++++++++++++++++++-
 src/blixemApp/blxcontext.hpp |  3 +++
 src/blixemApp/blxwindow.cpp  | 56 +++++++++++++++++++++++++++++++++-----------
 3 files changed, 91 insertions(+), 15 deletions(-)

2016-06-20  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/groups' into develop
2016-06-20  Gemma Guest  <gb10@sanger.ac.uk>
 Clear all groups not just quick groups - WIP
 src/blixemApp/blxwindow.cpp | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

2016-06-20  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/groups' into develop
2016-06-20  Gemma Guest  <gb10@sanger.ac.uk>
 Don't lose groups/filters when clearing - WIP
 src/blixemApp/blxcontext.cpp | 29 ++++++++++++++++++++++++++---
 src/blixemApp/blxcontext.hpp |  3 ++-
 src/blixemApp/blxwindow.cpp  | 23 +++++++++++++++--------
 3 files changed, 43 insertions(+), 12 deletions(-)

2016-06-20  Gemma Guest  <gb10@sanger.ac.uk>
 Don't highlight filtered seqs by default - WIP
 src/blixemApp/blxwindow.cpp | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

2016-06-15  Gemma Guest  <gb10@sanger.ac.uk>
 Fix error with bad access - REGRESSION FIX
 src/seqtoolsUtils/blxGff3Parser.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

2016-06-15  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/groups' into develop
2016-06-15  Gemma Guest  <gb10@sanger.ac.uk>
 Select clipboard features on startup
 src/blixemApp/blixem_.hpp   |  1 +
 src/blixemApp/blxwindow.cpp | 23 +++++++++++++++++++++--
 src/blixemApp/blxwindow.hpp |  1 +
 3 files changed, 23 insertions(+), 2 deletions(-)

2016-06-15  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/dotter_sfs' into develop
2016-06-15  Gemma Guest  <gb10@sanger.ac.uk>
 Fix badly displayed labels
 src/blixemApp/blxdotter.cpp     |  5 +--
 src/dotterApp/dotplot.cpp       | 81 ++++++++++++++++++++++++++++++++---------
 src/dotterApp/dotterMain.cpp    |  7 +++-
 src/seqtoolsUtils/blxmsp.cpp    |  1 -
 src/seqtoolsUtils/blxmsp.hpp    |  2 +-
 src/seqtoolsUtils/blxparser.cpp | 60 +++---------------------------
 6 files changed, 76 insertions(+), 80 deletions(-)

2016-06-14  Gemma Guest  <gb10@sanger.ac.uk>
 Fix minor compilation warning
 src/dotterApp/dotter.cpp | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

2016-06-14  Gemma Guest  <gb10@sanger.ac.uk>
 Minor fix to dotter feature series
 src/dotterApp/dotterMain.cpp    | 1 +
 src/seqtoolsUtils/blxparser.cpp | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

2016-06-15  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/groups' into develop
2016-06-13  Gemma Guest  <gb10@sanger.ac.uk>
 Fix edit groups dialog - REGRESSION FIX
 src/blixemApp/blxwindow.cpp | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

2016-06-13  Gemma Guest  <gb10@sanger.ac.uk>
 Replace old filter-ungrouped flags - WIP
 src/blixemApp/bigpicturegrid.cpp |  20 +-------
 src/blixemApp/blixem_.hpp        |   2 -
 src/blixemApp/blxcontext.cpp     | 105 +++++++++++++++++++++++++++++++++++----
 src/blixemApp/blxcontext.hpp     |   5 ++
 src/blixemApp/blxwindow.cpp      |  69 +++++++++++--------------
 src/blixemApp/detailviewtree.cpp |  35 ++-----------
 src/blixemApp/exonview.cpp       |  17 +------
 7 files changed, 135 insertions(+), 118 deletions(-)

2016-06-13  Gemma Guest  <gb10@sanger.ac.uk>
 Add option to add to existing quick group/filter - WIP
 src/blixemApp/blxcontext.cpp | 19 +++++++++++++++++++
 src/blixemApp/blxcontext.hpp |  1 +
 src/blixemApp/blxwindow.cpp  | 31 ++++++++++++++++++++++++-------
 3 files changed, 44 insertions(+), 7 deletions(-)

2016-06-13  Gemma Guest  <gb10@sanger.ac.uk>
 Replace match set group with 'quick' groups and filters - WIP
 src/blixemApp/blixem_.hpp    |   4 +
 src/blixemApp/blxcontext.cpp |  35 +++++--
 src/blixemApp/blxcontext.hpp |   2 +-
 src/blixemApp/blxwindow.cpp  | 226 ++++++++++++++++++++++---------------------
 4 files changed, 151 insertions(+), 116 deletions(-)

2016-05-18  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compile error if no sqlite3 - BUILD
 src/blixemApp/blxFetchDb.cpp | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

2016-05-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix use of uninitialised variable - TRIVIAL
 src/blixemApp/bigpicturegrid.cpp | 42 +++++++++++++++++++++++++++++-----------
 src/blixemApp/bigpicturegrid.hpp |  5 +++++
 2 files changed, 36 insertions(+), 11 deletions(-)

2016-05-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix call to invalid handler on exit - WIP
 src/blixemApp/blxmain.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-05-05  Gemma Guest  <gb10@sanger.ac.uk>
 Replace malloc with new for structs/classes - WIP
 src/belvuApp/belvu.cpp                 |  6 ++---
 src/belvuApp/belvuAlignment.cpp        |  4 ++--
 src/belvuApp/belvuConsPlot.cpp         |  4 ++--
 src/belvuApp/belvuTree.cpp             |  8 +++----
 src/belvuApp/belvuWindow.cpp           |  8 +++----
 src/blixemApp/bigpicture.cpp           |  4 ++--
 src/blixemApp/bigpicturegrid.cpp       |  4 ++--
 src/blixemApp/blxFetch.cpp             | 42 +++++++++++++++++++++++-----------
 src/blixemApp/blxcontext.cpp           |  4 ++--
 src/blixemApp/blxdotter.cpp            |  4 ++--
 src/blixemApp/blxmain.cpp              |  2 +-
 src/blixemApp/blxview.cpp              |  4 ++--
 src/blixemApp/blxwindow.cpp            | 12 +++++-----
 src/blixemApp/detailview.cpp           | 39 ++++++++++++++++---------------
 src/blixemApp/detailviewtree.cpp       |  8 +++----
 src/blixemApp/exonview.cpp             |  4 ++--
 src/blixemApp/sequencecellrenderer.cpp |  2 +-
 src/dotterApp/alignmenttool.cpp        |  8 +++----
 src/dotterApp/dotplot.cpp              |  4 ++--
 src/dotterApp/dotter.cpp               | 19 +++++++++------
 src/dotterApp/greyramptool.cpp         |  8 +++----
 src/dotterApp/seqtoolsExonView.cpp     |  4 ++--
 src/seqtoolsUtils/blxGff3Parser.cpp    |  6 ++---
 src/seqtoolsUtils/blxmsp.cpp           | 15 +++++++-----
 src/seqtoolsUtils/blxparser.cpp        |  2 +-
 src/seqtoolsUtils/seqtoolsFetch.cpp    |  2 +-
 src/seqtoolsUtils/utilities.cpp        | 12 +++++-----
 src/seqtoolsUtils/utilities.hpp        | 19 ++++++++-------
 28 files changed, 144 insertions(+), 114 deletions(-)

2016-05-04  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.43.0' into develop
2016-05-04  Gemma Guest  <gb10@sanger.ac.uk>
 Further fix to possible memory corruption - WIP
 src/dotterApp/dotter.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2016-05-04  Gemma Guest  <gb10@sanger.ac.uk>
 Attempt to fix memory corruption on mac - WIP
 src/blixemApp/blxwindow.cpp     |  6 ++++--
 src/seqtoolsUtils/blxmsp.cpp    |  9 +++++----
 src/seqtoolsUtils/utilities.cpp | 10 ----------
 src/seqtoolsUtils/utilities.hpp |  4 ----
 4 files changed, 9 insertions(+), 20 deletions(-)

2016-05-04  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compile errors when debug enabled - WIP
 src/blixemApp/detailview.cpp       | 4 ++--
 src/dotterApp/seqtoolsExonView.cpp | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

2016-05-04  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-70-g1b86 - Update RT and git commit reports
 src/ChangeLog | 7 +++++++
 1 file changed, 7 insertions(+)

2016-05-04  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-69-g4306 - Update RT and git commit reports
 src/ChangeLog                                  | 16 ++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 18 insertions(+), 1 deletion(-)

2016-05-03  Gemma Guest  <gb10@sanger.ac.uk>
 Attempt to fix crash on mac - REGRESSION FIX
 src/blixemApp/detailview.cpp | 29 ++++++++++++++++-------------
 1 file changed, 16 insertions(+), 13 deletions(-)

2016-05-03  Gemma Guest  <gb10@sanger.ac.uk>
 Revert "Revert "Remove to_string to fix compile error on FreeBSD - BUILD""
 src/blixemApp/detailview.cpp | 35 +++++++++++++++++------------------
 1 file changed, 17 insertions(+), 18 deletions(-)

2016-05-03  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-66-gc807 - Update RT and git commit reports
 src/ChangeLog                                  | 11 +++++++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 2 files changed, 12 insertions(+), 1 deletion(-)

2016-05-03  Gemma Guest  <gb10@sanger.ac.uk>
 Revert "Remove to_string to fix compile error on FreeBSD - BUILD"
 src/blixemApp/detailview.cpp | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

2016-04-28  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-64-gd36e - Update RT and git commit reports
 src/ChangeLog                                  | 5 +++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

2016-04-26  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-63-g8b3b - Update RT and git commit reports
 src/ChangeLog | 5 +++++
 1 file changed, 5 insertions(+)

2016-04-26  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-62-g70326 - Update RT and git commit reports
 src/ChangeLog | 5 +++++
 1 file changed, 5 insertions(+)

2016-04-26  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-61-gddeb - Update RT and git commit reports
 src/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

2016-04-26  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-60-g164e4 - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

2016-04-25  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.1-59-g125b - Update RT and git commit reports
 src/ChangeLog                                  | 8 ++++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

2016-04-22  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.43.0' into develop
2016-04-22  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'production' into release/4.43.0
2016-04-22  Gemma Guest  <gb10@sanger.ac.uk>
 Update release notes - DOC
 src/doc/User_doc/release_notes.html | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

2016-04-22  Gemma Guest  <gb10@sanger.ac.uk>
 Remove to_string to fix compile error on FreeBSD - BUILD
 src/blixemApp/detailview.cpp | 35 +++++++++++++++++------------------
 1 file changed, 17 insertions(+), 18 deletions(-)

2016-04-18  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.0-58-g0f579 - Update RT and git commit reports
 src/ChangeLog                          | 12 ++++++++++++
 src/build/release_docs/GIT_COMMITS.txt |  1 +
 2 files changed, 13 insertions(+)

2016-04-18  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.43.0' into develop
2016-04-18  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a typo which was causing drag-and-drop to fail - REGRESSION FIX
 src/blixemApp/blxwindow.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2016-04-18  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.0-56-g744c - Update RT and git commit reports
 src/ChangeLog                                  | 17 +++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 19 insertions(+), 1 deletion(-)

2016-04-18  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.43.0' into develop
2016-04-18  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a memory corruption crash on blixem startup - REGRESSION FIX
 src/blixemApp/blxwindow.cpp | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

2016-04-15  Steve Miller  <sm23@sanger.ac.uk>
 Release notes
 src/doc/User_doc/release_notes.html | 8 ++++++++
 1 file changed, 8 insertions(+)

2016-04-15  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.42.0-53-g8864 - Update RT and git commit reports
 src/ChangeLog                                  | 743 ++++++++++++++++---------
 src/build/release_docs/GIT_COMMITS.txt         |  14 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  12 +-
 3 files changed, 492 insertions(+), 277 deletions(-)

2016-04-08  Gemma Guest  <gb10@sanger.ac.uk>
 Update release notes for addition of c++0x in 4.41.0 - DOC
 src/doc/User_doc/release_notes.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-04-08  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a bug with big picture sections slightly misaligned - REGRESSION FIX
 src/blixemApp/bigpicture.cpp     | 2 +-
 src/blixemApp/bigpicturegrid.cpp | 2 +-
 src/blixemApp/exonview.cpp       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

2016-04-08  Gemma Guest  <gb10@sanger.ac.uk>
 Fix incorrect version number in release notes - DOC
 src/doc/User_doc/release_notes.html | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

2016-04-08  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/coverage' into develop - NEW FEATURE 'Detail view coverage'
2016-04-08  Gemma Guest  <gb10@sanger.ac.uk>
 Add option to display detail view coverage - WIP
 src/blixemApp/blxwindow.cpp | 30 ++++++++++++++++++++++++++----
 src/blixemApp/blxwindow.hpp |  3 ++-
 2 files changed, 28 insertions(+), 5 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Add comments about remaining tidying to be done - WIP
 src/blixemApp/coverageview.cpp | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Move highlight box functions to base class - WIP
 src/blixemApp/Makefile.am              |   2 +-
 src/blixemApp/bigpicture.cpp           | 276 ++++------------------------
 src/blixemApp/bigpicture.hpp           |  44 ++---
 src/blixemApp/bigpicturegrid.cpp       |  13 +-
 src/blixemApp/blxpanel.cpp             | 318 +++++++++++++++++++++++++++++++++
 src/blixemApp/blxpanel.hpp             |  53 +++++-
 src/blixemApp/blxwindow.cpp            |   9 +-
 src/blixemApp/coverageview.cpp         |  19 +-
 src/blixemApp/coverageview.hpp         |   4 +-
 src/blixemApp/detailview.cpp           |  90 ++++------
 src/blixemApp/detailview.hpp           |  17 +-
 src/blixemApp/detailviewtree.cpp       |  16 +-
 src/blixemApp/exonview.cpp             |  17 +-
 src/blixemApp/sequencecellrenderer.cpp |  16 +-
 14 files changed, 511 insertions(+), 383 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Add setting to change depth-per-cell for detail view coverage - WIP
 src/blixemApp/blxwindow.cpp | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Rename x position variable - WIP
 src/blixemApp/bigpicture.cpp     | 6 +++---
 src/blixemApp/bigpicture.hpp     | 2 +-
 src/blixemApp/bigpicturegrid.cpp | 2 +-
 src/blixemApp/blxpanel.hpp       | 2 +-
 src/blixemApp/coverageview.cpp   | 7 +++----
 src/blixemApp/coverageview.hpp   | 5 +----
 src/blixemApp/detailview.cpp     | 2 +-
 src/blixemApp/detailview.hpp     | 2 +-
 src/blixemApp/exonview.cpp       | 2 +-
 9 files changed, 13 insertions(+), 17 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Set highlight range for big picture panel - WIP
 src/blixemApp/bigpicture.cpp   | 14 ++++++++++++++
 src/blixemApp/bigpicture.hpp   |  1 +
 src/blixemApp/blxpanel.hpp     |  5 ++++-
 src/blixemApp/coverageview.cpp | 18 ++++++++++++++++--
 src/blixemApp/coverageview.hpp |  1 +
 5 files changed, 36 insertions(+), 3 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Move highlight-box calc to base class - WIP
 src/blixemApp/bigpicture.cpp     | 45 +---------------------------------------
 src/blixemApp/bigpicture.hpp     |  6 ------
 src/blixemApp/bigpicturegrid.cpp | 15 +++++++++++++-
 src/blixemApp/blxcontext.cpp     | 36 ++++++++++++++++++++++++++++++++
 src/blixemApp/blxcontext.hpp     |  4 ++++
 src/blixemApp/blxpanel.hpp       |  7 +++++++
 src/blixemApp/coverageview.cpp   | 44 ++++++++++++++++++++++++---------------
 src/blixemApp/coverageview.hpp   |  3 +--
 src/blixemApp/detailview.cpp     |  4 ----
 src/blixemApp/detailview.hpp     |  3 ---
 10 files changed, 90 insertions(+), 77 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Fix detail view coverage section width - WIP
 src/blixemApp/bigpicture.cpp   | 12 ++++++++++++
 src/blixemApp/bigpicture.hpp   |  1 +
 src/blixemApp/blixem_.hpp      |  8 ++++----
 src/blixemApp/blxpanel.hpp     |  2 +-
 src/blixemApp/blxview.cpp      |  8 ++++----
 src/blixemApp/blxwindow.cpp    |  4 ++--
 src/blixemApp/coverageview.cpp | 20 ++++++++++++++++++--
 src/blixemApp/coverageview.hpp |  3 ++-
 src/blixemApp/detailview.cpp   | 24 +++++++++++-------------
 src/blixemApp/detailview.hpp   |  1 +
 10 files changed, 56 insertions(+), 27 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Derive detail-view from BlxPanel - WIP
 src/blixemApp/detailview.cpp | 120 ++++++++++++++++++++++++++++++-------------
 src/blixemApp/detailview.hpp |   9 +++-
 2 files changed, 90 insertions(+), 39 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Add detail-view destructor - WIP
 src/blixemApp/detailview.cpp | 65 +++++++++++++++++++++++---------------------
 src/blixemApp/detailview.hpp |  5 ++++
 2 files changed, 39 insertions(+), 31 deletions(-)

2016-04-07  Gemma Guest  <gb10@sanger.ac.uk>
 Add base class for big picture - WIP
 src/blixemApp/Makefile.am        |  2 +-
 src/blixemApp/bigpicture.cpp     | 34 ++++++++++++++------------
 src/blixemApp/bigpicture.hpp     | 13 +++++++---
 src/blixemApp/bigpicturegrid.cpp |  2 +-
 src/blixemApp/blxpanel.hpp       | 53 ++++++++++++++++++++++++++++++++++++++++
 src/blixemApp/coverageview.cpp   | 19 ++++++++------
 src/blixemApp/coverageview.hpp   | 11 +++++++--
 src/blixemApp/exonview.cpp       |  2 +-
 8 files changed, 104 insertions(+), 32 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Coverage section has pointer to parent left border pos - WIP
 src/blixemApp/bigpicture.cpp     | 103 ++++++++++++++++++++++-----------------
 src/blixemApp/bigpicture.hpp     |   9 ++--
 src/blixemApp/bigpicturegrid.cpp |   2 +-
 src/blixemApp/coverageview.cpp   |  23 ++++++++-
 src/blixemApp/coverageview.hpp   |   5 ++
 src/blixemApp/exonview.cpp       |   2 +-
 6 files changed, 91 insertions(+), 53 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Remove unnecessary member variable - WIP
 src/blixemApp/bigpicture.cpp     |  2 --
 src/blixemApp/bigpicture.hpp     |  3 ---
 src/blixemApp/bigpicturegrid.cpp | 13 +++++--------
 src/blixemApp/blixem_.hpp        |  3 ++-
 src/blixemApp/coverageview.cpp   | 12 +++---------
 src/blixemApp/exonview.cpp       |  8 +++-----
 6 files changed, 13 insertions(+), 28 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Remove unnecessary member variable - WIP
 src/blixemApp/bigpicture.cpp     | 8 +++++---
 src/blixemApp/bigpicture.hpp     | 4 +++-
 src/blixemApp/bigpicturegrid.cpp | 2 +-
 src/blixemApp/coverageview.cpp   | 4 ++--
 4 files changed, 11 insertions(+), 7 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Remove char size from big picture - WIP
 src/blixemApp/bigpicture.cpp     | 49 +++++++++++++++++++++++++++++-----------
 src/blixemApp/bigpicture.hpp     | 11 ++++++---
 src/blixemApp/bigpicturegrid.cpp |  2 +-
 src/blixemApp/blxcontext.cpp     |  5 ++++
 src/blixemApp/blxcontext.hpp     |  1 +
 src/blixemApp/exonview.cpp       |  2 +-
 6 files changed, 52 insertions(+), 18 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Add char size to BlxContext - WIP
 src/blixemApp/blxcontext.cpp   | 11 +++++++++++
 src/blixemApp/blxcontext.hpp   | 16 +++++++++++++---
 src/blixemApp/coverageview.cpp | 13 ++++++++++++-
 src/blixemApp/coverageview.hpp |  1 +
 4 files changed, 37 insertions(+), 4 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Move sequence-group code to BlxContext file - WIP
 src/blixemApp/bigpicturegrid.cpp       |   2 +-
 src/blixemApp/blxcontext.cpp           | 116 ++++++++++++++++++++++++++++++
 src/blixemApp/blxcontext.hpp           |   8 ++-
 src/blixemApp/blxdotter.cpp            |  10 +--
 src/blixemApp/blxwindow.cpp            | 125 ++-------------------------------
 src/blixemApp/blxwindow.hpp            |   7 --
 src/blixemApp/detailview.cpp           |   4 +-
 src/blixemApp/detailviewtree.cpp       |   4 +-
 src/blixemApp/exonview.cpp             |   4 +-
 src/blixemApp/sequencecellrenderer.cpp |   4 +-
 10 files changed, 142 insertions(+), 142 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Add BlxContext destructor - WIP
 src/blixemApp/blxcontext.cpp    | 111 ++++++++++++++++++++++++++++-
 src/blixemApp/blxcontext.hpp    |   6 ++
 src/blixemApp/blxwindow.cpp     | 151 ++--------------------------------------
 src/seqtoolsUtils/utilities.cpp |  23 ++++++
 src/seqtoolsUtils/utilities.hpp |   2 +
 5 files changed, 147 insertions(+), 146 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Move code to BlxContext file - WIP
 src/blixemApp/blxcontext.cpp   | 333 +++++++++++++++++++++++++++++++++++++++-
 src/blixemApp/blxcontext.hpp   |   6 +-
 src/blixemApp/blxwindow.cpp    | 340 ++---------------------------------------
 src/blixemApp/blxwindow.hpp    |   2 -
 src/blixemApp/coverageview.cpp |   2 +-
 src/blixemApp/detailview.cpp   |  16 +-
 6 files changed, 354 insertions(+), 345 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Add BlxContext cpp file - WIP
 src/blixemApp/Makefile.am    |   2 +-
 src/blixemApp/blixem_.hpp    |   5 +-
 src/blixemApp/blxcontext.cpp | 350 +++++++++++++++++++++++++++++++++++++++++++
 src/blixemApp/blxcontext.hpp |   8 +-
 src/blixemApp/blxwindow.cpp  | 305 +------------------------------------
 5 files changed, 361 insertions(+), 309 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Move BlxContext to separate header - WIP
 src/blixemApp/Makefile.am              |   2 +-
 src/blixemApp/bigpicture.cpp           |   1 +
 src/blixemApp/bigpicturegrid.cpp       |   1 +
 src/blixemApp/blixem_.hpp              |  99 +----------------------
 src/blixemApp/blxFetch.cpp             |   1 +
 src/blixemApp/blxcontext.hpp           | 139 +++++++++++++++++++++++++++++++++
 src/blixemApp/blxdotter.cpp            |   1 +
 src/blixemApp/blxview.cpp              |   1 +
 src/blixemApp/blxwindow.cpp            |   1 +
 src/blixemApp/coverageview.cpp         |   1 +
 src/blixemApp/detailview.cpp           |   1 +
 src/blixemApp/detailviewtree.cpp       |   1 +
 src/blixemApp/exonview.cpp             |   1 +
 src/blixemApp/sequencecellrenderer.cpp |   1 +
 14 files changed, 155 insertions(+), 96 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compiler warnings - BUILD
 src/dotterApp/dotter.cpp | 2 --
 1 file changed, 2 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Add BlxContext constructor - WIP
 src/blixemApp/blixem_.hpp   |  16 +++
 src/blixemApp/blxwindow.cpp | 283 ++++++++++++++++++++++----------------------
 2 files changed, 155 insertions(+), 144 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Rename BlxContext - WIP
 src/blixemApp/bigpicture.cpp           |  24 ++--
 src/blixemApp/bigpicture.hpp           |   8 +-
 src/blixemApp/bigpicturegrid.cpp       |  20 ++--
 src/blixemApp/blixem_.hpp              |  16 +--
 src/blixemApp/blxFetch.cpp             |  14 +--
 src/blixemApp/blxdotter.cpp            |  86 +++++++-------
 src/blixemApp/blxview.cpp              |  22 ++--
 src/blixemApp/blxwindow.cpp            | 211 ++++++++++++++++-----------------
 src/blixemApp/blxwindow.hpp            |  16 +--
 src/blixemApp/coverageview.cpp         |   6 +-
 src/blixemApp/coverageview.hpp         |   6 +-
 src/blixemApp/detailview.cpp           | 124 +++++++++----------
 src/blixemApp/detailview.hpp           |   6 +-
 src/blixemApp/detailviewtree.cpp       |  34 +++---
 src/blixemApp/detailviewtree.hpp       |   2 +-
 src/blixemApp/exonview.cpp             |  20 ++--
 src/blixemApp/sequencecellrenderer.cpp |  12 +-
 17 files changed, 313 insertions(+), 314 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Convert context to class - WIP
 src/blixemApp/blixem_.hpp | 133 ++++++++++++++++++++++++----------------------
 1 file changed, 68 insertions(+), 65 deletions(-)

2016-04-06  Gemma Guest  <gb10@sanger.ac.uk>
 Remove deprecated register keyword - BUILD
 src/dotterApp/dotplot.cpp      | 20 ++++++++++----------
 src/dotterApp/dotterKarlin.cpp |  6 +++---
 2 files changed, 13 insertions(+), 13 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Add correct display range for detail view coverage - WIP
 src/blixemApp/bigpicture.cpp   |  4 +++
 src/blixemApp/coverageview.cpp | 78 ++++++++++++++++++++++--------------------
 src/blixemApp/coverageview.hpp | 30 ++++++++++------
 src/blixemApp/detailview.cpp   |  6 +++-
 4 files changed, 70 insertions(+), 48 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bugs with coverage view in detail view - WIP
 src/blixemApp/blxwindow.cpp    |  5 +++++
 src/blixemApp/coverageview.cpp | 10 ++++++----
 2 files changed, 11 insertions(+), 4 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Remove obsolete function - WIP
 src/blixemApp/bigpicture.cpp | 6 ------
 src/blixemApp/bigpicture.hpp | 1 -
 src/blixemApp/detailview.cpp | 6 ------
 src/blixemApp/detailview.hpp | 1 -
 4 files changed, 14 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Add coverage view to detail view - WIP
 src/blixemApp/blxwindow.cpp  |   1 +
 src/blixemApp/detailview.cpp | 250 ++++++++++++++++++++++++++-----------------
 src/blixemApp/detailview.hpp |  11 +-
 3 files changed, 161 insertions(+), 101 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Add constructor for detail view - WIP
 src/blixemApp/detailview.cpp | 197 ++++++++++++++++++++++++-------------------
 src/blixemApp/detailview.hpp |  17 ++++
 2 files changed, 128 insertions(+), 86 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bug with zooming to range - WIP
 src/blixemApp/bigpicture.cpp    | 3 ++-
 src/blixemApp/detailview.cpp    | 4 ++--
 src/dotterApp/alignmenttool.cpp | 6 ++++--
 src/seqtoolsUtils/blxmsp.cpp    | 4 ++--
 4 files changed, 10 insertions(+), 7 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix off-by-one in big picture drawing, and more tidying - WIP
 src/blixemApp/bigpicture.cpp           |  4 ++--
 src/blixemApp/blixem_.hpp              |  6 +++---
 src/blixemApp/blxFetch.cpp             |  8 ++++----
 src/blixemApp/blxwindow.cpp            |  4 ++--
 src/blixemApp/detailview.cpp           |  2 +-
 src/blixemApp/exonview.cpp             |  4 ++--
 src/blixemApp/sequencecellrenderer.cpp |  6 +++---
 src/seqtoolsUtils/blxmsp.cpp           | 14 ++++----------
 src/seqtoolsUtils/blxmsp.hpp           |  4 ++--
 9 files changed, 23 insertions(+), 29 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bug with drawing msps and more tidying - WIP
 src/blixemApp/bigpicture.cpp           |  9 ++--
 src/blixemApp/blixem_.hpp              |  6 +--
 src/blixemApp/blxFetch.cpp             |  8 +--
 src/blixemApp/blxdotter.cpp            |  8 +--
 src/blixemApp/blxmain.cpp              |  4 +-
 src/blixemApp/blxview.cpp              | 20 +++++---
 src/blixemApp/blxwindow.cpp            | 12 ++---
 src/blixemApp/detailview.cpp           | 14 ++---
 src/blixemApp/detailviewtree.cpp       |  2 +-
 src/blixemApp/sequencecellrenderer.cpp |  3 +-
 src/dotterApp/alignmenttool.cpp        |  9 ++--
 src/dotterApp/dotplot.cpp              |  4 +-
 src/seqtoolsUtils/blxGff3Parser.cpp    |  7 ++-
 src/seqtoolsUtils/blxmsp.cpp           | 62 +++++++++++++++--------
 src/seqtoolsUtils/blxmsp.hpp           |  4 +-
 src/seqtoolsUtils/blxparser.cpp        |  2 +-
 src/seqtoolsUtils/utilities.cpp        | 93 ++++++++++++++++++++++++++--------
 src/seqtoolsUtils/utilities.hpp        |  4 +-
 18 files changed, 172 insertions(+), 99 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bug with updating scroll range - WIP
 src/blixemApp/bigpicture.cpp       | 6 ++++--
 src/blixemApp/bigpicturegrid.cpp   | 9 ++-------
 src/blixemApp/blxview.cpp          | 7 +++++--
 src/blixemApp/exonview.cpp         | 9 ++-------
 src/dotterApp/seqtoolsExonView.cpp | 4 ++--
 5 files changed, 15 insertions(+), 20 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Use c++ bool values - WIP
 src/seqtoolsUtils/utilities.hpp | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bug with zooming due to intrange change - WIP
 src/blixemApp/bigpicture.cpp    |  2 +-
 src/seqtoolsUtils/utilities.cpp | 11 +++++++----
 2 files changed, 8 insertions(+), 5 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Remove accidental file - WIP
 src/blixemApp/sequencecellrenderer.cpp.~develop~ | 1612 ----------------------
 1 file changed, 1612 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a bug with new range access functions - WIP
 src/seqtoolsUtils/utilities.cpp | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a bug with unset ranges - WIP
 src/blixemApp/bigpicture.cpp           |  2 +-
 src/blixemApp/blxmain.cpp              |  4 +--
 src/blixemApp/blxview.cpp              | 15 +++++++--
 src/blixemApp/blxwindow.cpp            |  2 +-
 src/blixemApp/sequencecellrenderer.cpp |  8 ++---
 src/dotterApp/alignmenttool.cpp        |  1 -
 src/dotterApp/dotter.cpp               | 32 ++++++++++++-------
 src/seqtoolsUtils/blxGff3Parser.cpp    |  4 +--
 src/seqtoolsUtils/blxmsp.cpp           |  8 ++---
 src/seqtoolsUtils/blxparser.cpp        |  2 +-
 src/seqtoolsUtils/utilities.cpp        | 57 ++++++++++++++++++++++++++++------
 src/seqtoolsUtils/utilities.hpp        | 26 +++++++++++-----
 12 files changed, 112 insertions(+), 49 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Add utility function to simplify code - WIP
 src/blixemApp/bigpicture.cpp           | 25 ++++++++----------------
 src/blixemApp/blxmain.cpp              |  9 +++------
 src/blixemApp/blxview.cpp              | 19 +++++++-----------
 src/blixemApp/blxwindow.cpp            | 13 +++++--------
 src/blixemApp/detailview.cpp           | 16 ++++++----------
 src/blixemApp/sequencecellrenderer.cpp |  6 ++----
 src/dotterApp/alignmenttool.cpp        | 18 ++++++-----------
 src/dotterApp/dotplot.cpp              |  4 ++--
 src/dotterApp/dotter.cpp               | 12 ++++--------
 src/dotterApp/dotterMain.cpp           |  3 +--
 src/seqtoolsUtils/blxmsp.cpp           | 35 +++++++++++++---------------------
 src/seqtoolsUtils/blxparser.cpp        |  3 +--
 src/seqtoolsUtils/utilities.cpp        | 18 +++++++++++++----
 src/seqtoolsUtils/utilities.hpp        |  2 ++
 14 files changed, 74 insertions(+), 109 deletions(-)

2016-04-05  Gemma Guest  <gb10@sanger.ac.uk>
 Convert IntRange to class - WIP
 src/blixemApp/bigpicture.cpp           |  98 +++++++--------
 src/blixemApp/bigpicturegrid.cpp       |  38 +++---
 src/blixemApp/blxdotter.cpp            |  50 ++++----
 src/blixemApp/blxmain.cpp              |  16 +--
 src/blixemApp/blxview.cpp              |  80 ++++++------
 src/blixemApp/blxwindow.cpp            | 107 ++++++++--------
 src/blixemApp/coverageview.cpp         |   8 +-
 src/blixemApp/detailview.cpp           | 175 +++++++++++++-------------
 src/blixemApp/detailviewtree.cpp       |  50 ++++----
 src/blixemApp/exonview.cpp             |  15 ++-
 src/blixemApp/sequencecellrenderer.cpp |  50 ++++----
 src/dotterApp/alignmenttool.cpp        |  62 ++++-----
 src/dotterApp/dotplot.cpp              |  62 ++++-----
 src/dotterApp/dotter.cpp               |  58 ++++-----
 src/dotterApp/dotterMain.cpp           |   3 +-
 src/dotterApp/seqtoolsExonView.cpp     |   4 +-
 src/seqtoolsUtils/blxGff3Parser.cpp    |  28 ++---
 src/seqtoolsUtils/blxmsp.cpp           | 170 ++++++++++++-------------
 src/seqtoolsUtils/blxparser.cpp        |  18 +--
 src/seqtoolsUtils/utilities.cpp        | 222 +++++++++++++++++++++------------
 src/seqtoolsUtils/utilities.hpp        |  35 ++++--
 21 files changed, 716 insertions(+), 633 deletions(-)

2016-04-04  Gemma Guest  <gb10@sanger.ac.uk>
 Fix off-by-one error drawing coverage view - WIP
 src/blixemApp/coverageview.cpp | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

2016-03-11  Gemma Guest  <gb10@sanger.ac.uk>
 Convert coverage view to a class - WIP
 src/blixemApp/bigpicture.cpp     | 219 ++++++++++++++++++----------
 src/blixemApp/bigpicture.hpp     |  32 ++++-
 src/blixemApp/bigpicturegrid.cpp |   2 +-
 src/blixemApp/blxwindow.cpp      |  66 ++++++---
 src/blixemApp/coverageview.cpp   | 303 ++++++++++++++++++++++-----------------
 src/blixemApp/coverageview.hpp   |  48 +++++--
 6 files changed, 429 insertions(+), 241 deletions(-)

2016-03-11  Gemma Guest  <gb10@sanger.ac.uk>
 Convert to classes and add ptr to widget - WIP
 src/belvuApp/belvuAlignment.cpp  |  7 +++++--
 src/belvuApp/belvuConsPlot.cpp   | 43 +++++++++++++++++++++-------------------
 src/belvuApp/belvuTree.cpp       | 41 ++++++++++++++++++++------------------
 src/belvuApp/belvuWindow.cpp     | 34 ++++++++++++++++++-------------
 src/blixemApp/bigpicture.cpp     |  4 +++-
 src/blixemApp/bigpicture.hpp     | 10 ++++++----
 src/blixemApp/bigpicturegrid.cpp |  3 ++-
 src/blixemApp/bigpicturegrid.hpp |  1 +
 src/blixemApp/blxwindow.cpp      | 25 +++++++++++++----------
 src/blixemApp/coverageview.cpp   | 25 +++++++++++++----------
 src/blixemApp/detailview.cpp     |  7 +++++--
 src/blixemApp/detailview.hpp     |  1 +
 src/blixemApp/detailviewtree.cpp |  3 ++-
 src/blixemApp/detailviewtree.hpp |  3 ++-
 src/blixemApp/exonview.cpp       | 23 +++++++++++----------
 src/dotterApp/alignmenttool.cpp  | 16 ++++++++++-----
 src/dotterApp/dotplot.cpp        |  3 ++-
 src/dotterApp/dotter.cpp         |  7 +++++--
 src/dotterApp/dotter_.hpp        |  2 ++
 src/dotterApp/greyramptool.cpp   | 43 +++++++++++++++++++++-------------------
 20 files changed, 176 insertions(+), 125 deletions(-)

2016-03-11  Gemma Guest  <gb10@sanger.ac.uk>
 Convert properties structs to classes - WIP
 src/blixemApp/bigpicture.hpp     | 78 ++++++++++++++++++++--------------------
 src/blixemApp/bigpicturegrid.hpp | 25 ++++++-------
 src/blixemApp/detailview.hpp     |  5 +--
 src/blixemApp/detailviewtree.hpp | 23 ++++++------
 src/dotterApp/dotter_.hpp        | 78 ++++++++++++++++++++--------------------
 5 files changed, 108 insertions(+), 101 deletions(-)

2016-04-04  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'production' into develop
2016-04-04  Ed Griffiths  <edgrif@sanger.ac.uk>
 Update release notes. - DOC
 src/doc/User_doc/release_notes.html | 6 ++++++
 1 file changed, 6 insertions(+)

2016-04-04  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'production' into develop
2016-04-04  zmap  <zmap@sanger.ac.uk>
 Merge branch 'release/4.42.0' into production
2016-03-23  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.41.1-46-g0299 - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2016-03-17  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.41.1-45-gb1f4 - Update RT and git commit reports
 src/ChangeLog                                  | 368 ++++++++++++++++---------
 src/build/release_docs/GIT_COMMITS.txt         |  14 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  12 +-
 3 files changed, 264 insertions(+), 130 deletions(-)

2016-03-11  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/read_depth' into develop
2016-03-11  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compiler error on older gcc versions - BUILD
 src/blixemApp/detailview.cpp | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

2016-03-11  Gemma Guest  <gb10@sanger.ac.uk>
 Add read depth counters for N, gaps and unknown - WIP
 src/blixemApp/blixem_.hpp    |  8 ++++++--
 src/blixemApp/blxwindow.cpp  | 49 ++++++++++++++++++++++++++++++++++++++------
 src/blixemApp/detailview.cpp | 32 +++++++++++++++++++++++------
 3 files changed, 75 insertions(+), 14 deletions(-)

2016-03-11  Gemma Guest  <gb10@sanger.ac.uk>
 Make read depth display for active strand only - WIP
 src/blixemApp/blixem_.hpp    |  22 ++++--
 src/blixemApp/blxwindow.cpp  | 168 ++++++++++++++++++++++++++++++++++---------
 src/blixemApp/blxwindow.hpp  |   5 +-
 src/blixemApp/detailview.cpp |  21 ++++--
 4 files changed, 169 insertions(+), 47 deletions(-)

2016-03-10  Gemma Guest  <gb10@sanger.ac.uk>
 Read coverage now shows specific base support at coord - WIP
 src/blixemApp/blixem_.hpp    |  18 +++++++-
 src/blixemApp/blxwindow.cpp  | 102 +++++++++++++++++++++++++++++++++----------
 src/blixemApp/blxwindow.hpp  |   2 +-
 src/blixemApp/detailview.cpp |  31 ++++++++++++-
 4 files changed, 128 insertions(+), 25 deletions(-)

2016-03-10  Gemma Guest  <gb10@sanger.ac.uk>
 Update installation instructions - DOC
 src/INSTALL.linux   |  7 +++++--
 src/INSTALL.mac     |  7 +++++--
 src/INSTALL.windows | 41 +++++++++++++++++++++++++++++++++++------
 src/README          | 31 ++++++++++++++++++++++++-------
 4 files changed, 69 insertions(+), 17 deletions(-)

2016-03-10  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/read_depth
2016-03-09  Gemma Guest  <gb10@sanger.ac.uk>
 Minor improvement to installation instructions - RT 519841
 src/INSTALL.linux | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

2016-03-09  Gemma Guest  <gb10@sanger.ac.uk>
 Add README for generated files - BUILD
 src/build/release_docs/README | 4 ++++
 1 file changed, 4 insertions(+)

2016-03-09  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2016-03-09  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a C++ compilation error on cygwin - BUG FIX
 src/configure.ac | 1 -
 1 file changed, 1 deletion(-)

2016-03-09  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a C++ compilation error on cygwin - BUG FIX
 src/configure.ac | 1 -
 1 file changed, 1 deletion(-)

2016-03-02  zmap  <zmap@sanger.ac.uk>
 Merge branch 'release/4.41.0' into production
2016-03-01  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/read_depth
2016-03-01  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compile error on linux - REGRESSION FIX
 src/blixemApp/blxdotter.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-03-01  Gemma Guest  <gb10@sanger.ac.uk>
 Replace fprintf etc. with GLib functions - WIP
 src/blixemApp/blxdotter.cpp     | 159 +++++++++++++++++++---------------------
 src/seqtoolsUtils/blxmsp.cpp    | 151 ++++++++++++++++++++++++--------------
 src/seqtoolsUtils/blxmsp.hpp    |   6 +-
 src/seqtoolsUtils/utilities.cpp |  45 ++++++++----
 src/seqtoolsUtils/utilities.hpp |   2 +-
 5 files changed, 206 insertions(+), 157 deletions(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Replace mkstemp with g_mkstemp - TRIVIAL
 src/blixemApp/blxFetch.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Minor update to previous - WIP
 src/seqtoolsUtils/utilities.cpp | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/read_depth
2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Replace popen call with GLib function - REGRESSION FIX
 src/Makefile.am.common          |  4 +---
 src/seqtoolsUtils/utilities.cpp | 43 +++++++++++++++++------------------------
 2 files changed, 19 insertions(+), 28 deletions(-)

2016-02-29  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.40.0-25-g9d5a - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Revert "Revert "Fix ambiguous call to overloaded fn - REGRESSION FIX""
 src/blixemApp/detailview.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Revert "Revert "Remove deprecated-register flag (not avail on linux) - BUILD""
 src/Makefile.am.common | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Revert "Revert "Merge branch 'feature/read_depth' into develop - NEW FEATURE 'read depth'""
 src/blixemApp/blxwindow.cpp     |  45 ++++++
 src/blixemApp/blxwindow.hpp     |   3 +
 src/blixemApp/coverageview.cpp  |   2 +-
 src/blixemApp/detailview.cpp    | 349 ++++++++++++++++++++++++++++------------
 src/blixemApp/detailview.hpp    |   1 +
 src/seqtoolsUtils/utilities.cpp |  24 ++-
 src/seqtoolsUtils/utilities.hpp |   5 +-
 7 files changed, 319 insertions(+), 110 deletions(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Revert "Merge branch 'feature/read_depth' into develop - NEW FEATURE 'read depth'"
 src/blixemApp/blxwindow.cpp     |  45 ------
 src/blixemApp/blxwindow.hpp     |   3 -
 src/blixemApp/coverageview.cpp  |   2 +-
 src/blixemApp/detailview.cpp    | 349 ++++++++++++----------------------------
 src/blixemApp/detailview.hpp    |   1 -
 src/seqtoolsUtils/utilities.cpp |  24 +--
 src/seqtoolsUtils/utilities.hpp |   5 +-
 7 files changed, 110 insertions(+), 319 deletions(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Revert "Remove deprecated-register flag (not avail on linux) - BUILD"
 src/Makefile.am.common | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Revert "Fix ambiguous call to overloaded fn - REGRESSION FIX"
 src/blixemApp/detailview.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Fix ambiguous call to overloaded fn - REGRESSION FIX
 src/blixemApp/detailview.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2016-02-29  Gemma Guest  <gb10@sanger.ac.uk>
 Remove deprecated-register flag (not avail on linux) - BUILD
 src/Makefile.am.common | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/read_depth' into develop - NEW FEATURE 'read depth'
2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Add feedback box to display read depth - WIP
 src/blixemApp/blxwindow.cpp  | 30 +++++++++++++++++++++++++++++
 src/blixemApp/blxwindow.hpp  |  1 +
 src/blixemApp/detailview.cpp | 46 +++++++++++++++++++++++++++++++++++++-------
 3 files changed, 70 insertions(+), 7 deletions(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Add access function for read depth - WIP
 src/blixemApp/blxwindow.cpp    | 15 +++++++++++++++
 src/blixemApp/blxwindow.hpp    |  2 ++
 src/blixemApp/coverageview.cpp |  2 +-
 3 files changed, 18 insertions(+), 1 deletion(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Tooltips - TRIVIAL
 src/blixemApp/detailview.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Show selected match coord range in toolbar - WIP
 src/blixemApp/detailview.cpp | 112 +++++++++++++++++++++++++++----------------
 1 file changed, 72 insertions(+), 40 deletions(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Show selected coordinate range in feedback box - WIP
 src/blixemApp/detailview.cpp    | 64 +++++++++++++++++++++++++++++++++++------
 src/blixemApp/detailview.hpp    |  1 +
 src/seqtoolsUtils/utilities.cpp | 22 ++++++++++++++
 src/seqtoolsUtils/utilities.hpp |  3 ++
 4 files changed, 82 insertions(+), 8 deletions(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 More tidying/simplification - WIP
 src/blixemApp/detailview.cpp | 71 ++++++++++++++++++++++----------------------
 1 file changed, 36 insertions(+), 35 deletions(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 More reorganisation/tidying - WIP
 src/blixemApp/detailview.cpp    | 86 +++++++++++++++++++++--------------------
 src/seqtoolsUtils/utilities.cpp |  2 +-
 src/seqtoolsUtils/utilities.hpp |  2 +-
 3 files changed, 46 insertions(+), 44 deletions(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Tidying - split large function - WIP
 src/blixemApp/detailview.cpp | 126 +++++++++++++++++++++++++------------------
 1 file changed, 73 insertions(+), 53 deletions(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compile problem with popen on cygwin - BUILD
 src/Makefile.am.common | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Fix missing include - BUILD
 src/seqtoolsUtils/utilities.cpp | 1 +
 1 file changed, 1 insertion(+)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Disable deprecated-register warnings - BUILD
 src/Makefile.am.common | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compiler errors - BUILD
 src/seqtoolsUtils/seqtoolsWebBrowser.cpp | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

2016-02-26  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compiler errors on mac - BUILD
 src/belvuApp/belvuMain.cpp    | 10 +++++-----
 src/blixemApp/blxmain.cpp     |  8 ++++----
 src/dotterApp/dotterMain.cpp  |  8 ++++----
 src/seqtoolsUtils/version.hpp | 12 ++++++------
 4 files changed, 19 insertions(+), 19 deletions(-)

2016-02-25  Ed Griffiths  <edgrif@sanger.ac.uk>
 Ugh...what are these files about. - BUILD
 src/build/release_docs/GIT_COMMITS.txt         | 11 -----------
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  6 ------
 2 files changed, 17 deletions(-)

2016-02-25  Ed Griffiths  <edgrif@sanger.ac.uk>
 Change blixem to use new C++ pfetch obj. - DEVELOP
 src/blixemApp/blxFetch.cpp | 374 +++++++++++++++++++--------------------------
 1 file changed, 160 insertions(+), 214 deletions(-)

2016-02-25  Ed Griffiths  <edgrif@sanger.ac.uk>
 Fix clash with C++ identity keyword - TRIVIAL
 src/belvuApp/belvu.cpp     | 10 +++++-----
 src/belvuApp/belvuTree.cpp |  2 +-
 src/belvuApp/belvu_.hpp    |  2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

2016-02-25  Ed Griffiths  <edgrif@sanger.ac.uk>
 add -std to compiler flags. - BUILD
 src/Makefile.am.common | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-02-19  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.40.0-24-g382e - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2016-02-19  Gemma Guest  <gb10@sanger.ac.uk>
 Add links to the manuals from the User_doc directory - DOC
 src/doc/User_doc/Belvu_manual.pdf        | 1 +
 src/doc/User_doc/Blixem_manual.pdf       | 1 +
 src/doc/User_doc/Dotter_manual.pdf       | 1 +
 src/doc/User_doc/belvu_quick_start.html  | 2 +-
 src/doc/User_doc/blixem_quick_start.html | 2 +-
 src/doc/User_doc/dotter_quick_start.html | 2 +-
 src/doc/User_doc/manuals.html            | 6 +++---
 7 files changed, 9 insertions(+), 6 deletions(-)

2016-02-18  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.40.0-23-gd13eb - Update RT and git commit reports
 src/ChangeLog                                  | 368 +++++++++----------------
 src/build/release_docs/GIT_COMMITS.txt         |   8 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |   2 +-
 3 files changed, 129 insertions(+), 249 deletions(-)

2016-02-10  Ed Griffiths  <edgrif@sanger.ac.uk>
 Fxi gbtoools namespace - WIP
 src/blixemApp/blxFetch.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2016-02-05  Gemma Guest  <gb10@sanger.ac.uk>
 Remove obsolete gitignore placeholder - BUILD
 src/gbtools/.gitignore | 3 ---
 1 file changed, 3 deletions(-)

2016-02-05  Gemma Guest  <gb10@sanger.ac.uk>
 Fix gitignore and missing readme file for gbtools - BUILD
 src/.gitignore              |  2 ++
 src/autogen.sh              | 10 +++++-----
 src/gbtools/README_SEQTOOLS | 25 +++++++++++++++++++++++++
 3 files changed, 32 insertions(+), 5 deletions(-)

2016-02-04  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2016-02-03  zmap  <zmap@sanger.ac.uk>
 Merge branch 'release/4.40.0' into production
2016-01-28  Gemma Guest  <gb10@sanger.ac.uk>
 Fix to previous - REGRESSION FIX
 src/autogen.sh | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

2016-01-28  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a bug with conditional clone of gbtools - BUILD
 src/autogen.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-01-28  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.40.0' into develop
2016-01-26  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-38-gba23 - Update RT and git commit reports
 src/ChangeLog                                  | 28 ++++++++++++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 30 insertions(+), 1 deletion(-)

2016-01-25  Gemma Guest  <gb10@sanger.ac.uk>
 Add config option to set cainfo file location for curl - WIP
 src/blixemApp/blixem_.hpp        |  9 ++++++++-
 src/blixemApp/blxFetch.cpp       | 30 ++++++++++++++++++------------
 src/blixemApp/blxview.cpp        |  1 +
 src/blixemApp/blxwindow.cpp      |  3 +++
 src/blixemApp/detailview.cpp     |  9 +++++----
 src/blixemApp/detailviewtree.cpp |  8 ++++----
 src/libpfetch/libcurlobject.c    |  6 ++++++
 src/libpfetch/libpfetch.c        | 34 +++++++++++++++++++++++++++++++++-
 src/libpfetch/libpfetch_I.h      |  3 +++
 9 files changed, 81 insertions(+), 22 deletions(-)

2016-01-25  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bug where multiple pfetch windows open - REGRESSION FIX
 src/blixemApp/blixem_.hpp        |  6 ++++--
 src/blixemApp/blxFetch.cpp       | 39 +++++++++++++++++++++++----------------
 src/blixemApp/detailview.cpp     |  2 +-
 src/blixemApp/detailviewtree.cpp |  2 +-
 4 files changed, 29 insertions(+), 20 deletions(-)

2016-01-25  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-35-g2ffc4 - Update RT and git commit reports
 src/ChangeLog                                  | 15 +++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 17 insertions(+), 1 deletion(-)

2016-01-25  Gemma Guest  <gb10@sanger.ac.uk>
 Fix crash following libcurl error - REGRESSION FIX
 src/blixemApp/blxFetch.cpp | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

2016-01-25  Gemma Guest  <gb10@sanger.ac.uk>
 Fix minor error in runconfig script - BUILD
 src/runconfig.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-01-22  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-32-ged92 - Update RT and git commit reports
 src/ChangeLog | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

2016-01-22  Gemma Guest  <gb10@sanger.ac.uk>
 Minor fix to return status - WIP
 src/blixemApp/blxFetch.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2016-01-22  Gemma Guest  <gb10@sanger.ac.uk>
 Fix problem with previous - WIP
 src/blixemApp/blixem_.hpp   |  13 ++++
 src/blixemApp/blxFetch.cpp  | 165 ++++++++------------------------------------
 src/blixemApp/blxwindow.cpp |   5 +-
 src/libpfetch/libpfetch.c   |  19 +++--
 src/libpfetch/libpfetch_I.h |   2 +-
 5 files changed, 62 insertions(+), 142 deletions(-)

2016-01-22  Gemma Guest  <gb10@sanger.ac.uk>
 Add config for curl IP mode and debug - WIP
 src/blixemApp/blixem_.hpp           |  139 ++++-
 src/blixemApp/blxFetch.cpp          | 1166 +++++++++++++++++++----------------
 src/blixemApp/blxFetchDb.cpp        |   56 +-
 src/blixemApp/blxdotter.cpp         |    5 -
 src/blixemApp/blxview.cpp           |   19 +-
 src/blixemApp/blxwindow.cpp         |   32 +-
 src/blixemApp/detailview.cpp        |    8 +-
 src/blixemApp/detailviewtree.cpp    |    9 +-
 src/libpfetch/libcurlobject.c       |   12 +-
 src/libpfetch/libpfetch.c           |   80 +--
 src/libpfetch/libpfetch_I.h         |    4 +
 src/seqtoolsUtils/seqtoolsFetch.hpp |    4 +-
 12 files changed, 882 insertions(+), 652 deletions(-)

2016-01-22  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-28-g7203 - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2016-01-21  Ed Griffiths  <edgrif@sanger.ac.uk>
 Fix compiler includes as per gbtools - BUILD
 src/Makefile.am.common        | 14 ++++++++++++++
 src/belvuApp/Makefile.am      | 10 ++++++----
 src/blixemApp/Makefile.am     |  7 +------
 src/dotterApp/Makefile.am     |  7 +------
 src/runconfig.sh              |  9 ++++++++-
 src/seqtoolsUtils/Makefile.am |  7 +------
 6 files changed, 31 insertions(+), 23 deletions(-)

2016-01-20  Ed Griffiths  <edgrif@sanger.ac.uk>
 Fix small include slip up. - TRIVIAL
 src/blixemApp/blxFetch.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-01-20  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'feature/New_pfetch' into develop
2016-01-20  Ed Griffiths  <edgrif@sanger.ac.uk>
 Remove libpfetch itself from build. - BUILD
 src/libpfetch/Makefile.am             |   50 --
 src/libpfetch/libcurlobject.c         | 1095 ------------------------
 src/libpfetch/libcurlobject.h         |   87 --
 src/libpfetch/libcurlobject_I.h       |   98 ---
 src/libpfetch/libpfetch-cmarshal.c    |  131 ---
 src/libpfetch/libpfetch-cmarshal.h    |   35 -
 src/libpfetch/libpfetch-cmarshal.list |    2 -
 src/libpfetch/libpfetch-utils.c       |  114 ---
 src/libpfetch/libpfetch.c             | 1514 ---------------------------------
 src/libpfetch/libpfetch.h             |  165 ----
 src/libpfetch/libpfetch_I.h           |  249 ------
 src/libpfetch/libpfetch_P.h           |  133 ---
 12 files changed, 3673 deletions(-)

2016-01-20  Ed Griffiths  <edgrif@sanger.ac.uk>
 Fix stupid compiler warning. - TRIVIAL
 src/dotterApp/dotter.cpp | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

2016-01-20  Ed Griffiths  <edgrif@sanger.ac.uk>
 Remove local libpfetch from build. - BUILD
 src/blixemApp/Makefile.am | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

2016-01-20  Ed Griffiths  <edgrif@sanger.ac.uk>
 Remove local libpfetch from build. - BUILD
 src/Makefile.am  | 4 ----
 src/configure.ac | 3 +--
 2 files changed, 1 insertion(+), 6 deletions(-)

2016-01-19  Ed Griffiths  <edgrif@sanger.ac.uk>
 Put build back to use local pfetch until I convert gbtools code to C++ - BUILD
 src/Makefile.am           | 6 +++---
 src/blixemApp/Makefile.am | 3 ++-
 src/configure.ac          | 3 ++-
 3 files changed, 7 insertions(+), 5 deletions(-)

2016-01-18  Ed Griffiths  <edgrif@sanger.ac.uk>
 add new gbtools build stuff. - BUILD
 src/Makefile.am           | 28 +++++++++++++++++++++++++---
 src/belvuApp/Makefile.am  |  2 +-
 src/blixemApp/Makefile.am | 10 ++++++++--
 src/configure.ac          |  4 +++-
 src/dotterApp/Makefile.am |  2 +-
 src/runconfig.sh          |  2 +-
 6 files changed, 39 insertions(+), 9 deletions(-)

2016-01-18  Ed Griffiths  <edgrif@sanger.ac.uk>
 Fix up gbtools stuff. - BUILD
 src/autogen.sh | 80 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 78 insertions(+), 2 deletions(-)

2016-01-18  Ed Griffiths  <edgrif@sanger.ac.uk>
 Minor include change. - TRIVIAL
 src/blixemApp/blxmain.cpp | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

2016-01-18  Ed Griffiths  <edgrif@sanger.ac.uk>
 Fix trivial compile bug. - TRIVIAL
 src/blixemApp/blxFetch.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-01-18  Ed Griffiths  <edgrif@sanger.ac.uk>
 Small README for lib. - TRIVIAL
 src/gbtools/README | 14 --------------
 1 file changed, 14 deletions(-)

2016-01-18  Ed Griffiths  <edgrif@sanger.ac.uk>
 Fix small compiler warning. - TRIVIAL
 src/seqtoolsUtils/utilities.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2016-01-18  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.40.0' into develop
2016-01-15  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-27-g33fa - Update RT and git commit reports
 src/ChangeLog                                  | 10 ++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 12 insertions(+), 1 deletion(-)

2016-01-15  Gemma Guest  <gb10@sanger.ac.uk>
 Fix bug getting dataType config - REGRESSION FIX
 src/seqtoolsUtils/blxGff3Parser.cpp | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

2016-01-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-25-g7163 - Update RT and git commit reports
 src/ChangeLog | 5 +++++
 1 file changed, 5 insertions(+)

2016-01-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-24-gf54a - Update RT and git commit reports
 src/ChangeLog | 5 +++++
 1 file changed, 5 insertions(+)

2016-01-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-23-g4fc7 - Update RT and git commit reports
 src/ChangeLog | 5 +++++
 1 file changed, 5 insertions(+)

2016-01-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-22-g209e - Update RT and git commit reports
 src/ChangeLog | 5 +++++
 1 file changed, 5 insertions(+)

2016-01-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-21-ge639 - Update RT and git commit reports
 src/ChangeLog | 5 +++++
 1 file changed, 5 insertions(+)

2016-01-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-20-g9de16d - Update RT and git commit reports
 src/ChangeLog | 10 ++++++++++
 1 file changed, 10 insertions(+)

2016-01-14  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.40.0' into develop
2016-01-14  Gemma Guest  <gb10@sanger.ac.uk>
 Update release notes - DOC
 src/doc/User_doc/release_notes.html | 6 ++++++
 1 file changed, 6 insertions(+)

2016-01-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-18-gf028 - Update RT and git commit reports
 src/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

2016-01-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-17-g89ca - Update RT and git commit reports
 src/ChangeLog                                  | 72 ++++++++++++++++++++++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 2 files changed, 73 insertions(+), 1 deletion(-)

2016-01-14  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'develop' into release/4.40.0
2016-01-14  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.40.0' into develop
2015-12-22  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/bam' into develop - NEW FEATURE 'bam fetch'
2015-12-21  Gemma Guest  <gb10@sanger.ac.uk>
 Avoid memory leak - WIP
 src/seqtoolsUtils/blxGff3Parser.cpp | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

2015-12-21  Gemma Guest  <gb10@sanger.ac.uk>
 Unescape gff chars - WIP
 src/seqtoolsUtils/blxGff3Parser.cpp | 46 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 45 insertions(+), 1 deletion(-)

2015-12-21  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compile error on linux - REGRESSION FIX
 src/belvuApp/belvuTree.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-12-21  Gemma Guest  <gb10@sanger.ac.uk>
 Fix error conditionally compiling html code - BUILD
 src/seqtoolsUtils/Makefile.am       | 4 ++++
 src/seqtoolsUtils/seqtoolsFetch.hpp | 8 ++++----
 2 files changed, 8 insertions(+), 4 deletions(-)

2015-12-21  Gemma Guest  <gb10@sanger.ac.uk>
 Pass fetch command in gff tag - WIP
 src/blixemApp/blixem_.hpp           |  52 +-------------
 src/blixemApp/blxFetch.cpp          | 134 +++++++++++++++++-------------------
 src/blixemApp/blxmain.cpp           |   5 +-
 src/blixemApp/blxview.cpp           |   2 +-
 src/dotterApp/dotterMain.cpp        |   2 +-
 src/seqtoolsUtils/Makefile.am       |   2 +-
 src/seqtoolsUtils/blxGff3Parser.cpp | 126 ++++++++++++++++++++++++++++-----
 src/seqtoolsUtils/blxGff3Parser.hpp |   3 +-
 src/seqtoolsUtils/blxparser.cpp     |  21 +++---
 src/seqtoolsUtils/blxparser.hpp     |   2 +-
 src/seqtoolsUtils/seqtoolsFetch.cpp |  62 +++++++++++++++++
 src/seqtoolsUtils/seqtoolsFetch.hpp |  97 ++++++++++++++++++++++++++
 12 files changed, 351 insertions(+), 157 deletions(-)

2015-12-21  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compiler error with min/max macros - BUILD
 src/belvuApp/belvuAlignment.cpp    | 13 ++++++++-----
 src/belvuApp/belvuConsPlot.cpp     |  9 ++++++---
 src/belvuApp/belvuTree.cpp         |  7 +++++--
 src/belvuApp/belvuWindow.cpp       |  9 ++++++---
 src/blixemApp/bigpicture.cpp       |  4 ++++
 src/blixemApp/bigpicturegrid.cpp   |  3 +++
 src/blixemApp/blxFetch.cpp         |  2 ++
 src/blixemApp/blxdotter.cpp        |  4 ++++
 src/blixemApp/blxview.cpp          |  3 +++
 src/blixemApp/blxwindow.cpp        |  4 ++++
 src/blixemApp/detailview.cpp       |  4 ++++
 src/blixemApp/detailviewtree.cpp   |  3 +++
 src/blixemApp/exonview.cpp         |  4 ++++
 src/dotterApp/dotplot.cpp          |  4 ++++
 src/dotterApp/dotter.cpp           |  4 ++++
 src/dotterApp/seqtoolsExonView.cpp |  4 ++++
 src/seqtoolsUtils/blxmsp.cpp       |  3 +++
 src/seqtoolsUtils/utilities.cpp    |  4 ++++
 src/seqtoolsUtils/utilities.hpp    |  3 ---
 19 files changed, 75 insertions(+), 16 deletions(-)

2015-12-18  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-7-gca231 - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

2015-12-17  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-6-g80aa - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2015-12-15  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.39.3-5-g053c - Update RT and git commit reports
 src/ChangeLog                                  | 61 ++++++++------------------
 src/build/release_docs/GIT_COMMITS.txt         |  4 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 22 +---------
 3 files changed, 22 insertions(+), 65 deletions(-)

2015-12-09  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/pfetch' into develop - NEW FEATURE 'pfetch errors'
2015-12-09  Gemma Guest  <gb10@sanger.ac.uk>
 Report libcurl errors - WIP
 src/blixemApp/blxFetch.cpp | 27 +++++++++++++++++++++------
 1 file changed, 21 insertions(+), 6 deletions(-)

2015-12-09  Gemma Guest  <gb10@sanger.ac.uk>
 Add function to return curl error - WIP
 src/libpfetch/libcurlobject.c |  6 +++-
 src/libpfetch/libpfetch.c     | 75 +++++++++++++++++++++++++------------------
 src/libpfetch/libpfetch.h     |  1 +
 3 files changed, 50 insertions(+), 32 deletions(-)

2015-12-07  Gemma Guest  <gb10@sanger.ac.uk>
 Warn if connection closed without response - WIP
 src/blixemApp/blxFetch.cpp    | 107 +++++++++++++++++++++++++++++++++++++++---
 src/libpfetch/libcurlobject.c |  23 +++++----
 2 files changed, 114 insertions(+), 16 deletions(-)

2015-11-30  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-11-30  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'develop' into production
2015-11-30  Gemma Guest  <gb10@sanger.ac.uk>
 Update release notes - DOC
 src/doc/User_doc/release_notes.html | 8 ++++++++
 1 file changed, 8 insertions(+)

2015-11-30  Gemma Guest  <gb10@sanger.ac.uk>
 Further improvement to handling of transparent styles - NEW FEATURE 'styles'
 src/seqtoolsUtils/blxmsp.cpp    |  39 +++++++----
 src/seqtoolsUtils/utilities.cpp | 145 ++++++++++++++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.hpp |  17 ++++-
 3 files changed, 185 insertions(+), 16 deletions(-)

2015-11-25  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-11-25  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'develop' into production
2015-11-25  Gemma Guest  <gb10@sanger.ac.uk>
 Update release notes for  - DOC
 src/doc/User_doc/release_notes.html | 8 ++++++++
 1 file changed, 8 insertions(+)

2015-11-24  Gemma Guest  <gb10@sanger.ac.uk>
 Improvment on previous to use border color for fill - WIP
 src/seqtoolsUtils/blxmsp.cpp | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

2015-11-24  Gemma Guest  <gb10@sanger.ac.uk>
 Don't allow transparent colours on the detail view - NEW FEATURE 'styles'
 src/blixemApp/sequencecellrenderer.cpp | 13 ++++++-
 src/seqtoolsUtils/blxmsp.cpp           | 64 ++++++++++++++++++++++++++--------
 src/seqtoolsUtils/blxmsp.hpp           |  3 +-
 3 files changed, 63 insertions(+), 17 deletions(-)

2015-11-11  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-11-11  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'develop' into production
2015-11-11  Gemma Guest  <gb10@sanger.ac.uk>
 Update release notes - DOC
 src/doc/User_doc/release_notes.html | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

2015-11-11  Gemma Guest  <gb10@sanger.ac.uk>
 Don't initialise the display in command-line mode - BUG FIX
 src/belvuApp/belvu.cpp     |  7 +++----
 src/belvuApp/belvuMain.cpp | 11 ++++++++---
 src/belvuApp/belvu_.hpp    |  2 ++
 3 files changed, 13 insertions(+), 7 deletions(-)

2015-11-02  zmap  <zmap@sanger.ac.uk>
 Merge branch 'release/4.39.0' into production
2015-10-27  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.38.0-9-g7b2ef - Update RT and git commit reports
 src/ChangeLog                                  | 5 +++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

2015-10-19  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.38.0-8-g31bb - Update RT and git commit reports
 src/ChangeLog | 5 +++++
 1 file changed, 5 insertions(+)

2015-10-19  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.38.0-7-g731d - Update RT and git commit reports
 src/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

2015-10-19  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.38.0-6-g370e - Update RT and git commit reports
 src/ChangeLog                                  | 5 +++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

2015-10-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.38.0-5-g03a9 - Update RT and git commit reports
 src/ChangeLog | 7 +++++++
 1 file changed, 7 insertions(+)

2015-10-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.38.0-4-gae89 - Update RT and git commit reports
 src/ChangeLog                                  | 89 +++++---------------------
 src/build/release_docs/GIT_COMMITS.txt         |  7 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 22 +++----
 3 files changed, 28 insertions(+), 90 deletions(-)

2015-10-12  Gemma Guest  <gb10@sanger.ac.uk>
 Fix missing install docs - DOC
 src/INSTALL.DEVELOPER | 100 ++++++++++++++++++++++++++++++++++++++++++++++++++
 src/Makefile.am       |   2 +-
 2 files changed, 101 insertions(+), 1 deletion(-)

2015-10-09  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-10-09  Gemma Guest  <gb10@sanger.ac.uk>
 Update release notes for 4.37.0 and 4.38.0 - DOC
 src/doc/User_doc/release_notes.html | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

2015-09-29  zmap  <zmap@sanger.ac.uk>
 Merge branch 'release/4.38.0' into production
2015-09-23  Gemma Guest  <gb10@sanger.ac.uk>
 Avoid potential null accesses - TRIVIAL
 src/dotterApp/alignmenttool.cpp | 213 +++++++++++++++++++++++++++-------------
 1 file changed, 143 insertions(+), 70 deletions(-)

2015-09-16  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.37.0-15-g244b - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2015-09-14  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.37.0-14-gb1fc - Update RT and git commit reports
 src/ChangeLog                                  | 88 ++++++++++++++++++++------
 src/build/release_docs/GIT_COMMITS.txt         |  7 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 12 ++--
 3 files changed, 79 insertions(+), 28 deletions(-)

2015-09-01  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'production' into develop
2015-09-01  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'release/4.37' into production
2015-08-24  Gemma Guest  <gb10@sanger.ac.uk>
 Fix to previous - gtk_main_quit was failing - WIP
 src/blixemApp/blxFetch.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2015-08-24  Gemma Guest  <gb10@sanger.ac.uk>
 Temp fix for problem with infinite 'Bad file descriptor' messages RT '485625'
 src/blixemApp/blxFetch.cpp | 34 +++++++++++++++++++++++++++++-----
 1 file changed, 29 insertions(+), 5 deletions(-)

2015-08-20  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.36-5-g91ee - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2015-08-18  Gemma Guest  <gb10@sanger.ac.uk>
 Fix an issue where maybe-canonical option wasn't being saved - WIP
 src/blixemApp/blixem_.hpp   | 1 +
 src/blixemApp/blxwindow.cpp | 1 +
 2 files changed, 2 insertions(+)

2015-08-18  Gemma Guest  <gb10@sanger.ac.uk>
 Fix a bug with colinearity lines when cigar string contains introns - BUG FIX
 src/seqtoolsUtils/blxGff3Parser.cpp | 13 +++++++++++--
 src/seqtoolsUtils/blxmsp.cpp        | 18 +++++++++++++-----
 src/seqtoolsUtils/blxmsp.hpp        |  2 +-
 3 files changed, 25 insertions(+), 8 deletions(-)

2015-08-17  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/settings' into develop
2015-08-17  Gemma Guest  <gb10@sanger.ac.uk>
 Add a button to save settings rather than saving on exit - WIP
 src/blixemApp/blxwindow.cpp | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

2015-08-17  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'feature/splice_sites' into develop
2015-08-17  Gemma Guest  <gb10@sanger.ac.uk>
 Disable highlighting of maybe-canonical splice sites by default - WIP
 src/blixemApp/blxwindow.cpp | 1 -
 1 file changed, 1 deletion(-)

2015-08-17  Gemma Guest  <gb10@sanger.ac.uk>
 Add tooltip text for settings options - NEW FEATURE 'Tooltips'
 src/blixemApp/blxwindow.cpp | 139 +++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 123 insertions(+), 16 deletions(-)

2015-08-17  Gemma Guest  <gb10@sanger.ac.uk>
 Make highlighting of maybe-canonical splice sites optional - WIP
 src/blixemApp/blixem_.hpp    | 1 +
 src/blixemApp/blxwindow.cpp  | 5 ++++-
 src/blixemApp/detailview.cpp | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

2015-08-17  Gemma Guest  <gb10@sanger.ac.uk>
 Implement highlighting for maybe-canonical splice sites - WIP
 src/blixemApp/blxwindow.cpp  |   2 +-
 src/blixemApp/detailview.cpp | 127 ++++++++++++++++++++++++++++++++++---------
 src/blixemApp/detailview.hpp |   6 ++
 3 files changed, 107 insertions(+), 28 deletions(-)

2015-08-17  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.36-4-g79d7 - Update RT and git commit reports
 src/ChangeLog                                  | 92 +++-----------------------
 src/build/release_docs/GIT_COMMITS.txt         |  7 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 22 ++++--
 3 files changed, 29 insertions(+), 92 deletions(-)

2015-08-17  Gemma Guest  <gb10@sanger.ac.uk>
 Add colour for maybe-canonical highlighting - WIP
 src/blixemApp/blixem_.hpp   | 3 +++
 src/blixemApp/blxwindow.cpp | 1 +
 2 files changed, 4 insertions(+)

2015-08-17  Gemma Guest  <gb10@sanger.ac.uk>
 Make sure we only set proxy from config if given - TRIVIAL
 src/blixemApp/blxFetch.cpp | 22 +++++++++++++++-------
 src/libpfetch/libpfetch.c  | 21 ++++++++++++++++++++-
 2 files changed, 35 insertions(+), 8 deletions(-)

2015-08-11  Gemma Guest  <gb10@sanger.ac.uk>
 Add tooltips to feedback boxes - TRIVIAL
 src/blixemApp/detailview.cpp | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

2015-08-11  Gemma Guest  <gb10@sanger.ac.uk>
 There are now separate feedback boxes for seq name and coords - NEW FEATURE 'Feedback box'
 src/blixemApp/detailview.cpp | 179 ++++++++++++++++++++++++++++++++-----------
 1 file changed, 133 insertions(+), 46 deletions(-)

2015-08-04  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-08-04  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.36' into production
2015-07-29  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.35-15-g96fd - Update RT and git commit reports
 src/ChangeLog                                  | 5 +++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

2015-07-23  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.35-14-g2d13 - Update RT and git commit reports
 src/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

2015-07-23  Gemma Guest  <gb10@sanger.ac.uk>
 Merge branch 'release/4.36' into develop
2015-07-23  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.35-13-g2f52 - Update RT and git commit reports
 src/ChangeLog                                  | 16 ++++++++++++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 2 files changed, 17 insertions(+), 1 deletion(-)

2015-07-22  Gemma Guest  <gb10@sanger.ac.uk>
 Add facility to set proxy from config file - WIP
 src/blixemApp/blixem_.hpp     |  2 ++
 src/blixemApp/blxFetch.cpp    |  4 ++++
 src/blixemApp/detailview.cpp  | 37 +------------------------------------
 src/libpfetch/libcurlobject.c |  5 +++++
 src/libpfetch/libpfetch.c     | 22 ++++++++++++++++++++++
 src/libpfetch/libpfetch_I.h   |  2 ++
 6 files changed, 36 insertions(+), 36 deletions(-)

2015-07-17  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.35-11-g5cab - Update RT and git commit reports
 src/ChangeLog                                  | 12 ++++++++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)

2015-07-15  Gemma Guest  <gb10@sanger.ac.uk>
 Update release notes - DOC
 src/doc/User_doc/release_notes.html | 5 +++++
 1 file changed, 5 insertions(+)

2015-07-15  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.35-9-gfbc6 - Update RT and git commit reports
 src/ChangeLog                                  | 154 ++++++-------------------
 src/build/release_docs/GIT_COMMITS.txt         |   9 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  52 +--------
 3 files changed, 40 insertions(+), 175 deletions(-)

2015-07-15  Gemma Guest  <gb10@sanger.ac.uk>
 Remove unnecessary realize step - TRIVIAL
 src/blixemApp/detailview.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2015-07-15  Gemma Guest  <gb10@sanger.ac.uk>
 fix incorrect return status in http fetch - TRIVIAL
 src/blixemApp/blxFetch.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-06-26  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'production' into develop
2015-06-26  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'release/4.35' into production
2015-06-24  Gemma Guest  <gb10@sanger.ac.uk>
 Minor change to error message format - TRIVIAL
 src/blixemApp/blxFetch.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-06-24  Gemma Guest  <gb10@sanger.ac.uk>
 Improve error reporting in http fetch - NEW FEATURE 'Error reporting'
 src/blixemApp/blxFetch.cpp  | 150 +++++++++++++++++++++++++++-----------------
 src/libpfetch/libpfetch.c   |  46 +++++++++-----
 src/libpfetch/libpfetch.h   |   2 +-
 src/libpfetch/libpfetch_I.h |   2 +-
 4 files changed, 125 insertions(+), 75 deletions(-)

2015-06-23  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.34.7-25-g04a2 - Update RT and git commit reports
 src/ChangeLog                                  | 16 ++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 18 insertions(+), 1 deletion(-)

2015-06-23  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compiler warnings and add logging for pfetch fix - TRIVIAL
 src/libpfetch/libcurlobject.c | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

2015-06-19  Gemma Guest  <gb10@sanger.ac.uk>
 Fix for http-pfetch on trusty - RT 474213
 src/libpfetch/libcurlobject.c | 96 ++++++++++++++++++++++++++-----------------
 1 file changed, 59 insertions(+), 37 deletions(-)

2015-06-23  Gemma Guest  <gb10@sanger.ac.uk>
 Fix compiler warnings and add logging for pfetch fix - TRIVIAL
 src/libpfetch/libcurlobject.c | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

2015-06-19  Gemma Guest  <gb10@sanger.ac.uk>
 Fix for http-pfetch on trusty - RT 474213
 src/libpfetch/libcurlobject.c | 96 ++++++++++++++++++++++++++-----------------
 1 file changed, 59 insertions(+), 37 deletions(-)

2015-06-19  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.34.7-22-ge741 - Update RT and git commit reports
 src/ChangeLog                                  | 5 +++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

2015-06-18  Gemma Guest  <gb10@sanger.ac.uk>
 Reduce max size of gdk window to help avoid crashing - BUG FIX
 src/dotterApp/dotplot.cpp | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

2015-06-18  Gemma Guest  <gb10@sanger.ac.uk>
 Attach error handlers for dotter and belvu - NEW FEATURE 'Error handling'
 src/belvuApp/belvuMain.cpp   | 4 ++++
 src/dotterApp/dotterMain.cpp | 5 +++++
 2 files changed, 9 insertions(+)

2015-06-16  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.34.7-21-gb08b - Update RT and git commit reports
 src/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

2015-06-16  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.34.7-20-gd9bc - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

2015-06-15  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.34.7-19-g3430a - Update RT and git commit reports
 src/ChangeLog                                  | 5 +++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

2015-06-11  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.34.7-18-g1513 - Update RT and git commit reports
 src/ChangeLog | 12 ++++++++++++
 1 file changed, 12 insertions(+)

2015-06-11  Steve Miller  <sm23@sanger.ac.uk>
 edit of release notes - DOC
 src/doc/User_doc/release_notes.html | 9 +++++++++
 1 file changed, 9 insertions(+)

2015-06-11  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.34.7-16-gacf2 - Update RT and git commit reports
 src/ChangeLog                                  | 16 ++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 12 +++++++++++-
 3 files changed, 28 insertions(+), 1 deletion(-)

2015-06-11  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'release/4.35' into develop
2015-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into release/4.35
2015-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes for 4.34.7 - DOC
 src/doc/User_doc/release_notes.html | 5 +++++
 1 file changed, 5 insertions(+)

2015-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with sorting by similarity/identity to first sequence - RT 473624
 src/belvuApp/belvuMain.cpp | 2 ++
 1 file changed, 2 insertions(+)

2015-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with sorting by similarity/identity to first sequence - RT 473624
 src/belvuApp/belvuMain.cpp | 2 ++
 1 file changed, 2 insertions(+)

2015-05-19  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.34.1-11-ge787 - Update RT and git commit reports
 src/ChangeLog | 7 +++++++
 1 file changed, 7 insertions(+)

2015-05-19  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.34.1-10-g5aa6 - Update RT and git commit reports
 src/ChangeLog                                  | 698 ++-----------------------
 src/build/release_docs/GIT_COMMITS.txt         |  19 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  50 +-
 3 files changed, 83 insertions(+), 684 deletions(-)

2015-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'hotfix/4.34.4' into production
2015-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix build problem from latest changes - REGRESSION FIX
 src/test/scripts/manual/Makefile.am | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix missing makefiles from previous - BUILD
 src/configure.ac | 12 ++++++++++++
 1 file changed, 12 insertions(+)

2015-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Add test and examples directories back into dist - BUILD
 src/Makefile.am                               |   2 +-
 src/examples/Makefile.am                      |  11 ++-
 src/test/Makefile.am                          |   4 +-
 src/test/data/Makefile.am                     |  35 ++++++++
 src/test/scripts/Makefile.am                  |   8 ++
 src/test/scripts/automated/Makefile.am        |   8 ++
 src/test/scripts/automated/belvu/Makefile.am  | 111 ++++++++++++++++++++++++++
 src/test/scripts/automated/blixem/Makefile.am |  12 +++
 src/test/scripts/automated/dotter/Makefile.am |  15 ++++
 src/test/scripts/manual/Makefile.am           |   8 ++
 src/test/scripts/manual/belvu/Makefile.am     |   8 ++
 src/test/scripts/manual/blixem/Makefile.am    |   8 ++
 src/test/scripts/manual/dotter/Makefile.am    |   8 ++
 13 files changed, 234 insertions(+), 4 deletions(-)

2015-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix build problem from latest changes - REGRESSION FIX
 src/test/scripts/manual/Makefile.am | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix missing makefiles from previous - BUILD
 src/configure.ac | 12 ++++++++++++
 1 file changed, 12 insertions(+)

2015-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Add test and examples directories back into dist - BUILD
 src/Makefile.am                               |   2 +-
 src/examples/Makefile.am                      |  11 ++-
 src/test/Makefile.am                          |   4 +-
 src/test/data/Makefile.am                     |  35 ++++++++
 src/test/scripts/Makefile.am                  |   8 ++
 src/test/scripts/automated/Makefile.am        |   8 ++
 src/test/scripts/automated/belvu/Makefile.am  | 111 ++++++++++++++++++++++++++
 src/test/scripts/automated/blixem/Makefile.am |  12 +++
 src/test/scripts/automated/dotter/Makefile.am |  15 ++++
 src/test/scripts/manual/Makefile.am           |   8 ++
 src/test/scripts/manual/belvu/Makefile.am     |   8 ++
 src/test/scripts/manual/blixem/Makefile.am    |   8 ++
 src/test/scripts/manual/dotter/Makefile.am    |   8 ++
 13 files changed, 234 insertions(+), 4 deletions(-)

2015-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'hotfix/4.34.2' into production
2015-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes for 4.34.2 - DOC
 src/doc/User_doc/release_notes.html | 5 +++++
 1 file changed, 5 insertions(+)

2015-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Fix dependency problem when compiling with multiple threads - RT 467905
 src/belvuApp/Makefile.am  | 10 ++--------
 src/blixemApp/Makefile.am | 10 ++--------
 src/dotterApp/Makefile.am | 10 ++--------
 3 files changed, 6 insertions(+), 24 deletions(-)

2015-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Fix compiler warnings to do with signed char indices - BUILD
 src/belvuApp/belvu.cpp | 366 ++++++++++++++++++++++++-------------------------
 1 file changed, 183 insertions(+), 183 deletions(-)

2015-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Fix dependency problem when compiling with multiple threads - RT 467905
 src/belvuApp/Makefile.am  | 10 ++--------
 src/blixemApp/Makefile.am | 10 ++--------
 src/dotterApp/Makefile.am | 10 ++--------
 3 files changed, 6 insertions(+), 24 deletions(-)

2015-05-01  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-05-01  Gemma Barson  <gb10@sanger.ac.uk>
 Minor fix to version numbering - BUILD
 src/autogen.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-05-01  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-05-01  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.34' into production
2015-04-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix minor typo in gbtools gitignore - TRIVIAL
 src/gbtools/.gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-04-24  Gemma Barson  <gb10@sanger.ac.uk>
 Add gbtools README file - BUILD
 src/gbtools/.gitignore |  3 +++
 src/gbtools/README     | 14 ++++++++++++++
 2 files changed, 17 insertions(+)

2015-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Make annoying popup a warning instead - TRIVIAL
 src/blixemApp/sequencecellrenderer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-04-20  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.33-89-g0b24 - Update RT and git commit reports
 src/ChangeLog                                  | 30 ++++++++++++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 32 insertions(+), 1 deletion(-)

2015-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Better fix for codon highlighting - REGRESSION FIX
 src/blixemApp/blxwindow.cpp      |  12 +--
 src/blixemApp/detailview.cpp     | 161 ++++++++++++++++++++++++---------------
 src/blixemApp/detailview.hpp     |   3 +-
 src/blixemApp/detailviewtree.cpp |   4 +-
 4 files changed, 107 insertions(+), 73 deletions(-)

2015-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Improve highlighting of selected sequence range - WIP
 src/blixemApp/sequencecellrenderer.cpp | 28 ++++++++++++++++++++--------
 1 file changed, 20 insertions(+), 8 deletions(-)

2015-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fix minor bug with codon highlighting in protein blixem - REGRESSION FIX
 src/blixemApp/detailview.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes - DOC
 src/doc/User_doc/release_notes.html | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2015-04-17  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.33-84-g81fd - Update RT and git commit reports
 src/ChangeLog                                  | 1053 ++++++++++++------------
 src/build/release_docs/GIT_COMMITS.txt         |   27 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |   32 +-
 3 files changed, 597 insertions(+), 515 deletions(-)

2015-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 DNA search now highlights the result range - NEW FEATURE 'DNA search'
 src/blixemApp/blxwindow.cpp | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes - DOC
 src/doc/User_doc/release_notes.html | 4 ++++
 1 file changed, 4 insertions(+)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fix crash pressing Esc on undocked tool - BUG FIX
 src/dotterApp/dotter.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Minor updates to docs - DOC
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf | Bin 1084518 -> 1060576 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex |   4 ++--
 src/doc/User_doc/blixem_quick_start.html         |  10 +++++-----
 3 files changed, 7 insertions(+), 7 deletions(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Update blixem manual for v34 - DOC
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf   | Bin 1058892 -> 1084518 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex   | 148 +++++++++------------
 .../User_doc/Blixem_manual/img_view_variations.png | Bin 14011 -> 13714 bytes
 3 files changed, 63 insertions(+), 85 deletions(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Update test plan - DOC
 src/test/test_plan.ods | Bin 43903 -> 44092 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/select_sequence' into develop
2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Update test plan - WIP
 src/test/test_plan.ods | Bin 36611 -> 43903 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Minor fixes to selections in dna header - WIP
 src/blixemApp/detailview.cpp     | 22 +++++++++++++++++-----
 src/blixemApp/detailviewtree.cpp | 29 -----------------------------
 src/seqtoolsUtils/utilities.cpp  | 30 ++++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.hpp  |  2 ++
 4 files changed, 49 insertions(+), 34 deletions(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Update release docs for recent features - DOC
 src/doc/User_doc/release_notes.html | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/select_sequence' into develop
2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Retain selection range after toggling strand - WIP
 src/blixemApp/detailview.cpp | 35 +++++++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 10 deletions(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fix minor issues extending and trimming selection - WIP
 src/blixemApp/detailview.cpp | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 better way of getting modifiers - WIP
 src/blixemApp/bigpicturegrid.cpp | 5 ++---
 src/blixemApp/detailview.cpp     | 3 +--
 src/blixemApp/detailviewtree.cpp | 5 ++---
 src/blixemApp/exonview.cpp       | 5 ++---
 4 files changed, 7 insertions(+), 11 deletions(-)

2015-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fix problem with re-centering not being disabled - WIP
 src/blixemApp/detailview.cpp | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

2015-04-15  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/select_sequence' into develop
2015-04-15  Gemma Barson  <gb10@sanger.ac.uk>
 Update test plan with new sequence selection stuff and snp track scrolling - DOC
 src/test/test_plan.ods | Bin 38902 -> 36611 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2015-04-15  Gemma Barson  <gb10@sanger.ac.uk>
 Improve highlighting of selected sequence - WIP
 src/blixemApp/sequencecellrenderer.cpp | 69 +++++++++++++++++++++-------------
 1 file changed, 43 insertions(+), 26 deletions(-)

2015-04-15  Gemma Barson  <gb10@sanger.ac.uk>
 Improve highlighting of selected sequence in headers - WIP
 src/blixemApp/detailview.cpp     | 38 ++++++++++++++++++++++++++++++++------
 src/blixemApp/detailview.hpp     |  1 +
 src/blixemApp/detailviewtree.cpp | 21 ++++++++++++++++++++-
 3 files changed, 53 insertions(+), 7 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/select_sequence' into develop - RT 457600
2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Comments - TRIVIAL
 src/blixemApp/blxwindow.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with copying translation in dna mode - WIP
 src/blixemApp/blxwindow.cpp | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Change keyboard shortcuts for new options - WIP
 src/blixemApp/blxwindow.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Add sequence context menu to dna header - WIP
 src/blixemApp/blxwindow.cpp      | 36 +++++++++-------------
 src/blixemApp/blxwindow.hpp      |  2 +-
 src/blixemApp/detailview.cpp     | 65 ++++++++++++++++++++++++++++++++++++++--
 src/blixemApp/detailviewtree.cpp |  4 +--
 4 files changed, 79 insertions(+), 28 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Add context menu for tree header - WIP
 src/blixemApp/blxwindow.cpp            | 205 ++++++++++++++++++++++++++++-----
 src/blixemApp/blxwindow.hpp            |   1 +
 src/blixemApp/detailview.cpp           | 100 +++++++++++-----
 src/blixemApp/detailview.hpp           |   6 +-
 src/blixemApp/detailviewtree.cpp       |  55 +++++++--
 src/blixemApp/sequencecellrenderer.cpp |  15 ++-
 6 files changed, 312 insertions(+), 70 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Refactoring - WIP
 src/blixemApp/detailviewtree.cpp | 69 ++++++++++++++++++++++++++--------------
 1 file changed, 45 insertions(+), 24 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix shift-click selections - WIP
 src/blixemApp/detailview.cpp | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Use selection range for copy-by-mark - WIP
 src/blixemApp/blxwindow.cpp | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix problem with background not being highlighted for range - WIP
 src/blixemApp/sequencecellrenderer.cpp | 34 ++++++++++++++++++++++++++--------
 1 file changed, 26 insertions(+), 8 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Set last-selected coord as main selection coord - WIP
 src/blixemApp/blxwindow.cpp  | 27 ++-------------------------
 src/blixemApp/detailview.cpp | 16 +++++++++++-----
 src/blixemApp/detailview.hpp |  1 +
 3 files changed, 14 insertions(+), 30 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Use Alt instead of Shift to move by one dna base - WIP
 src/blixemApp/blxwindow.cpp | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

2015-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Add functionality to select a range of coords - WIP
 src/blixemApp/blxview.cpp              |   4 +-
 src/blixemApp/blxwindow.cpp            | 167 ++++++++++-----
 src/blixemApp/detailview.cpp           | 357 ++++++++++++++++++++++++---------
 src/blixemApp/detailview.hpp           | 108 +++++-----
 src/blixemApp/detailviewtree.cpp       |  52 +++--
 src/blixemApp/sequencecellrenderer.cpp |   6 +-
 6 files changed, 483 insertions(+), 211 deletions(-)

2015-04-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix direction of copied string - WIP
 src/blixemApp/blxwindow.cpp | 65 ++++++++++++++++++++++++++++++++++++---------
 1 file changed, 52 insertions(+), 13 deletions(-)

2015-04-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug in calculating msp coords - REGRESSION FIX
 src/blixemApp/blxview.cpp                        |    3 +
 src/blixemApp/detailview.cpp                     |    8 +-
 src/blixemApp/sequencecellrenderer.cpp.~develop~ | 1612 ++++++++++++++++++++++
 3 files changed, 1620 insertions(+), 3 deletions(-)

2015-04-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with rev strand - WIP
 src/blixemApp/blxwindow.cpp | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

2015-04-10  Gemma Barson  <gb10@sanger.ac.uk>
 Add function to copy a section of a match sequence - WIP
 src/blixemApp/blixem_.hpp              |   5 +-
 src/blixemApp/blxview.cpp              |  59 ++++++++++-----
 src/blixemApp/blxwindow.cpp            | 134 ++++++++++++++++++++++++++++++++-
 src/blixemApp/detailview.cpp           |   4 +-
 src/blixemApp/sequencecellrenderer.cpp |   6 +-
 5 files changed, 180 insertions(+), 28 deletions(-)

2015-04-10  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/snp_track' into develop - RT 457103
2015-04-10  Gemma Barson  <gb10@sanger.ac.uk>
 Make horizontal mouse-wheel scrolling work for the whole detail view - WIP
 src/blixemApp/detailview.cpp     | 40 ++++++++++++++++++++++++++++++++++++++--
 src/blixemApp/detailviewtree.cpp | 36 ------------------------------------
 2 files changed, 38 insertions(+), 38 deletions(-)

2015-04-10  Gemma Barson  <gb10@sanger.ac.uk>
 Add independent cache for multiple snp splitter bar positions - WIP
 src/blixemApp/detailview.cpp     | 106 +++++++++++++++++++++++++++++++--------
 src/blixemApp/detailview.hpp     |   1 -
 src/blixemApp/detailviewtree.cpp |   8 +--
 3 files changed, 88 insertions(+), 27 deletions(-)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Remove obsolete function to calculate snp track size - WIP"
 src/blixemApp/detailview.cpp | 48 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 Double-clicking ref seq resets snp track size - WIP
 src/blixemApp/detailview.cpp | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 Enable/disable snp track when it becomes visible/hidden by splitter - WIP
 src/blixemApp/detailview.cpp     | 45 ++++++++++++++++++++++++++++++++++++++--
 src/blixemApp/detailview.hpp     |  2 +-
 src/blixemApp/detailviewtree.cpp |  2 +-
 3 files changed, 45 insertions(+), 4 deletions(-)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 refactoring - WIP
 src/blixemApp/detailview.cpp     | 44 ++++++++++++++++++++++++----------------
 src/blixemApp/detailview.hpp     |  1 +
 src/blixemApp/detailviewtree.cpp | 24 ++++++----------------
 3 files changed, 33 insertions(+), 36 deletions(-)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 Remove obsolete function to calculate snp track size - WIP
 src/blixemApp/detailview.cpp | 48 --------------------------------------------
 1 file changed, 48 deletions(-)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 Double-click minimised snp track pane - WIP
 src/blixemApp/detailview.cpp | 147 ++++++++++++++++++++++++-------------------
 src/blixemApp/detailview.hpp |   1 +
 2 files changed, 84 insertions(+), 64 deletions(-)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 Make snp scroll step one char height - WIP
 src/blixemApp/detailview.cpp | 90 +++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 88 insertions(+), 2 deletions(-)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fix problem with scroll window size - WIP
 src/blixemApp/detailview.cpp     | 30 ++++++++++--------------------
 src/blixemApp/detailviewtree.cpp |  3 +++
 2 files changed, 13 insertions(+), 20 deletions(-)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 Make paned window available in snp resize function - WIP
 src/blixemApp/detailview.cpp     | 94 ++++++++++++++++++++++++++++------------
 src/blixemApp/detailview.hpp     |  1 +
 src/blixemApp/detailviewtree.cpp |  3 +-
 3 files changed, 69 insertions(+), 29 deletions(-)

2015-04-09  Gemma Barson  <gb10@sanger.ac.uk>
 Improve debug output - TRIVIAL
 src/blixemApp/bigpicture.cpp     |   4 -
 src/blixemApp/bigpicturegrid.cpp |   8 --
 src/blixemApp/detailview.cpp     | 187 ++++++++++++++++++++++++++++++++++++---
 src/blixemApp/exonview.cpp       |   8 --
 4 files changed, 176 insertions(+), 31 deletions(-)

2015-04-08  Gemma Barson  <gb10@sanger.ac.uk>
 Put snp track in scrollwin (not working yet) - WIP
 src/blixemApp/detailview.cpp     | 56 +++++++++++++++++++++++++++++-----------
 src/blixemApp/detailview.hpp     |  1 +
 src/blixemApp/detailviewtree.cpp |  8 +++++-
 3 files changed, 49 insertions(+), 16 deletions(-)

2015-04-08  Gemma Barson  <gb10@sanger.ac.uk>
 Put individual trees inside a frame - WIP
 src/blixemApp/detailview.cpp     |  4 ++--
 src/blixemApp/detailviewtree.cpp | 17 ++++++++++++-----
 2 files changed, 14 insertions(+), 7 deletions(-)

2015-04-08  Gemma Barson  <gb10@sanger.ac.uk>
 Make snp track resizable (dna mode) - WIP
 src/blixemApp/detailview.cpp     |  3 +-
 src/blixemApp/detailviewtree.cpp | 77 ++++++++++++++++++++++------------------
 src/blixemApp/detailviewtree.hpp |  1 -
 3 files changed, 44 insertions(+), 37 deletions(-)

2015-04-08  Gemma Barson  <gb10@sanger.ac.uk>
 Remove unused variable - TRIVIAL
 src/blixemApp/detailview.hpp | 1 -
 1 file changed, 1 deletion(-)

2015-04-08  Gemma Barson  <gb10@sanger.ac.uk>
 Make snp track resizable (protein mode) - WIP
 src/blixemApp/detailview.cpp     | 82 ++++++++++++++++++++--------------------
 src/blixemApp/detailview.hpp     |  3 +-
 src/blixemApp/detailviewtree.cpp |  8 +---
 3 files changed, 45 insertions(+), 48 deletions(-)

2015-03-26  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'production' into develop
2015-03-26  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'release/4.33' into production
2015-03-24  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.32.1-41-g732d - Update RT and git commit reports
 src/ChangeLog | 5 +++++
 1 file changed, 5 insertions(+)

2015-03-24  Gemma Barson  <gb10@sanger.ac.uk>
 Add gbtools version string to about dialog - NEW FEATURE 'Version strings'
 src/belvuApp/belvu.cpp        | 14 ++++++++++++--
 src/belvuApp/belvu_.hpp       |  7 +------
 src/blixemApp/blixem_.hpp     | 10 +++-------
 src/blixemApp/blxview.cpp     | 15 ++++++++++++---
 src/blixemApp/blxwindow.cpp   |  4 ++++
 src/dotterApp/dotter.cpp      | 12 ++++++++++--
 src/dotterApp/dotter_.hpp     |  6 +-----
 src/seqtoolsUtils/version.hpp |  2 +-
 8 files changed, 44 insertions(+), 26 deletions(-)

2015-03-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fix compilation problem with gbtools subdir - BUILD
 .gitignore       |  2 +-
 src/autogen.sh   | 22 ++++++++++++++++++++++
 src/configure.ac |  6 ++----
 3 files changed, 25 insertions(+), 5 deletions(-)

2015-03-24  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.32.1-40-g9ea7 - Update RT and git commit reports
 src/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

2015-03-24  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.32.1-39-g3fcd - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

2015-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Minor name change of generated file - TRIVIAL
 src/autogen.sh   | 2 +-
 src/configure.ac | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

2015-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Improve the way we get the git version number - BUILD
 .gitignore     |  3 +++
 src/autogen.sh | 16 +++++++++++++++-
 src/version.m4 |  1 -
 3 files changed, 18 insertions(+), 2 deletions(-)

2015-03-19  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.32.1-38-gd7c9 - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

2015-03-18  Gemma Barson  <gb10@sanger.ac.uk>
 Update build documentation with notes on gbtools - DOC
 src/doc/Design_notes/build.html | 3 +++
 1 file changed, 3 insertions(+)

2015-03-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug in runconfig script where it didn't recognise cmd line flags - BUILD
 src/runconfig.sh | 86 +++++++++++++++++++++++++++++---------------------------
 1 file changed, 45 insertions(+), 41 deletions(-)

2015-03-18  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/gbtools' into develop
2015-03-18  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.32.1-37-gb867 - Update RT and git commit reports
 src/ChangeLog                                  | 6 ++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

2015-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Use main gbtools header - BUILD
 src/belvuApp/belvuConsPlot.cpp  | 2 +-
 src/belvuApp/belvuTree.cpp      | 2 +-
 src/belvuApp/belvuWindow.cpp    | 2 +-
 src/blixemApp/blxdotter.cpp     | 2 +-
 src/blixemApp/blxwindow.cpp     | 2 +-
 src/dotterApp/dotter.cpp        | 2 +-
 src/seqtoolsUtils/utilities.cpp | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

2015-03-16  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.32.1-36-g2d57 - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2015-03-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix compile error on cygwin - BUILD
 src/belvuApp/Makefile.am  | 4 +++-
 src/blixemApp/Makefile.am | 5 ++++-
 src/dotterApp/Makefile.am | 5 ++++-
 3 files changed, 11 insertions(+), 3 deletions(-)

2015-03-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix compilation of gbtools in subdir - BUILD
 src/configure.ac              | 3 +--
 src/seqtoolsUtils/Makefile.am | 7 ++++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

2015-03-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix compile order error on linux - BUILD
 src/belvuApp/Makefile.am  | 2 +-
 src/blixemApp/Makefile.am | 2 +-
 src/dotterApp/Makefile.am | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

2015-03-13  Gemma Barson  <gb10@sanger.ac.uk>
 Tidy makefiles - BUILD
 src/belvuApp/Makefile.am  | 20 ++++++++++++++++----
 src/blixemApp/Makefile.am | 17 ++++++++++++++---
 src/dotterApp/Makefile.am | 17 ++++++++++++++---
 3 files changed, 44 insertions(+), 10 deletions(-)

2015-03-13  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/gbtools
2015-03-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix hang on linux, regression caused by c++ changes - BUG FIX
 src/blixemApp/sequencecellrenderer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Revert "Fix installation of docs in dist file - BUILD""
 src/configure.ac                         |  4 ++++
 src/doc/Design_notes/Makefile.am         | 13 +++++++++++++
 src/doc/Design_notes/modules/Makefile.am | 13 +++++++++++++
 src/doc/Makefile.am                      |  2 +-
 4 files changed, 31 insertions(+), 1 deletion(-)

2015-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Revert "Fix missing docs installation - BUILD""
 src/Makefile.am | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2015-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Revert "Merge branch 'feature/cpp' into develop""
 src/Makefile.am                                    | 103 +--------------------
 src/belvuApp/Makefile.am                           |  23 +++++
 src/belvuApp/{belvu.c => belvu.cpp}                |  20 ++--
 .../{belvuAlignment.c => belvuAlignment.cpp}       |   8 +-
 .../{belvuAlignment.h => belvuAlignment.hpp}       |   2 +-
 .../{belvuConsPlot.c => belvuConsPlot.cpp}         |   6 +-
 .../{belvuConsPlot.h => belvuConsPlot.hpp}         |   2 +-
 src/belvuApp/{belvuMain.c => belvuMain.cpp}        |  10 +-
 src/belvuApp/{belvuTree.c => belvuTree.cpp}        |   6 +-
 src/belvuApp/{belvuTree.h => belvuTree.hpp}        |   2 +-
 src/belvuApp/{belvuWindow.c => belvuWindow.cpp}    |  10 +-
 src/belvuApp/{belvuWindow.h => belvuWindow.hpp}    |   2 +-
 src/belvuApp/{belvu_.h => belvu_.hpp}              |   6 +-
 src/blixemApp/Makefile.am                          |  45 +++++++++
 src/blixemApp/{bigpicture.c => bigpicture.cpp}     |  12 +--
 src/blixemApp/{bigpicture.h => bigpicture.hpp}     |   6 +-
 .../{bigpicturegrid.c => bigpicturegrid.cpp}       |  12 +--
 .../{bigpicturegrid.h => bigpicturegrid.hpp}       |   4 +-
 src/blixemApp/{blixem_.h => blixem_.hpp}           |   6 +-
 src/blixemApp/{blxFetch.c => blxFetch.cpp}         |  23 +++--
 src/blixemApp/{blxFetchDb.c => blxFetchDb.cpp}     |   6 +-
 src/blixemApp/{blxdotter.c => blxdotter.cpp}       |  23 ++---
 src/blixemApp/{blxdotter.h => blxdotter.hpp}       |   2 +-
 src/blixemApp/{blxmain.c => blxmain.cpp}           |   8 +-
 src/blixemApp/{blxview.c => blxview.cpp}           |  20 ++--
 src/blixemApp/{blxview.h => blxview.hpp}           |   0
 src/blixemApp/{blxwindow.c => blxwindow.cpp}       |  28 +++---
 src/blixemApp/{blxwindow.h => blxwindow.hpp}       |   4 +-
 src/blixemApp/{coverageview.c => coverageview.cpp} |   8 +-
 src/blixemApp/{coverageview.h => coverageview.hpp} |   2 +-
 src/blixemApp/{detailview.c => detailview.cpp}     |  14 +--
 src/blixemApp/{detailview.h => detailview.hpp}     |   4 +-
 .../{detailviewtree.c => detailviewtree.cpp}       |  14 +--
 .../{detailviewtree.h => detailviewtree.hpp}       |   6 +-
 src/blixemApp/{exonview.c => exonview.cpp}         |  16 ++--
 src/blixemApp/{exonview.h => exonview.hpp}         |   2 +-
 ...encecellrenderer.c => sequencecellrenderer.cpp} |  14 +--
 ...encecellrenderer.h => sequencecellrenderer.hpp} |   2 +-
 src/configure.ac                                   |  11 ++-
 src/doc/Makefile.am                                |   8 ++
 src/doc/User_doc/Makefile.am                       |  22 +++++
 src/dotterApp/Makefile.am                          |  23 +++++
 .../{alignmenttool.c => alignmenttool.cpp}         |   4 +-
 src/dotterApp/{dotplot.c => dotplot.cpp}           |   6 +-
 src/dotterApp/{dotter.c => dotter.cpp}             |  18 ++--
 src/dotterApp/{dotter.h => dotter.hpp}             |   2 +-
 src/dotterApp/{dotterKarlin.c => dotterKarlin.cpp} |   2 +-
 src/dotterApp/{dotterMain.c => dotterMain.cpp}     |  13 +--
 src/dotterApp/{dotter_.h => dotter_.hpp}           |   4 +-
 src/dotterApp/{greyramptool.c => greyramptool.cpp} |   4 +-
 .../{seqtoolsExonView.c => seqtoolsExonView.cpp}   |   6 +-
 .../{seqtoolsExonView.h => seqtoolsExonView.hpp}   |   4 +-
 src/examples/Makefile.am                           |   8 ++
 src/libpfetch/Makefile.am                          |  50 ++++++++++
 src/libpfetch/libcurlobject.h                      |   9 +-
 src/libpfetch/libcurlobject_I.h                    |  10 ++
 src/libpfetch/libpfetch-cmarshal.h                 |   7 ++
 src/libpfetch/libpfetch.h                          |   8 ++
 src/libpfetch/libpfetch_I.h                        |   8 ++
 src/libpfetch/libpfetch_P.h                        |   8 ++
 src/seqtoolsUtils/Makefile.am                      |  14 +++
 .../{blxGff3Parser.c => blxGff3Parser.cpp}         |   8 +-
 .../{blxGff3Parser.h => blxGff3Parser.hpp}         |   2 +-
 src/seqtoolsUtils/{blxmsp.c => blxmsp.cpp}         |   6 +-
 src/seqtoolsUtils/{blxmsp.h => blxmsp.hpp}         |   2 +-
 src/seqtoolsUtils/{blxparser.c => blxparser.cpp}   |  16 ++--
 src/seqtoolsUtils/{blxparser.h => blxparser.hpp}   |   0
 src/seqtoolsUtils/{iupac.h => iupac.hpp}           |   0
 ...seqtoolsWebBrowser.c => seqtoolsWebBrowser.cpp} |   2 +-
 src/seqtoolsUtils/{translate.c => translate.cpp}   |   4 +-
 src/seqtoolsUtils/{utilities.c => utilities.cpp}   |   2 +-
 src/seqtoolsUtils/{utilities.h => utilities.hpp}   |   1 -
 src/seqtoolsUtils/{version.h => version.hpp}       |   0
 src/test/Makefile.am                               |   8 ++
 74 files changed, 476 insertions(+), 305 deletions(-)

2015-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.33' into develop
2015-03-12  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.32.1-35-gcfe0 - Update RT and git commit reports
 src/ChangeLog                                  | 161 +++++++++++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |   2 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  10 ++
 3 files changed, 173 insertions(+)

2015-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Merge branch 'feature/cpp' into develop"
 src/Makefile.am                                    | 103 ++++++++++++++++++++-
 src/belvuApp/Makefile.am                           |  23 -----
 src/belvuApp/{belvu.cpp => belvu.c}                |  20 ++--
 .../{belvuAlignment.cpp => belvuAlignment.c}       |   8 +-
 .../{belvuAlignment.hpp => belvuAlignment.h}       |   2 +-
 .../{belvuConsPlot.cpp => belvuConsPlot.c}         |   6 +-
 .../{belvuConsPlot.hpp => belvuConsPlot.h}         |   2 +-
 src/belvuApp/{belvuMain.cpp => belvuMain.c}        |  10 +-
 src/belvuApp/{belvuTree.cpp => belvuTree.c}        |   6 +-
 src/belvuApp/{belvuTree.hpp => belvuTree.h}        |   2 +-
 src/belvuApp/{belvuWindow.cpp => belvuWindow.c}    |  10 +-
 src/belvuApp/{belvuWindow.hpp => belvuWindow.h}    |   2 +-
 src/belvuApp/{belvu_.hpp => belvu_.h}              |   6 +-
 src/blixemApp/Makefile.am                          |  45 ---------
 src/blixemApp/{bigpicture.cpp => bigpicture.c}     |  12 +--
 src/blixemApp/{bigpicture.hpp => bigpicture.h}     |   6 +-
 .../{bigpicturegrid.cpp => bigpicturegrid.c}       |  12 +--
 .../{bigpicturegrid.hpp => bigpicturegrid.h}       |   4 +-
 src/blixemApp/{blixem_.hpp => blixem_.h}           |   6 +-
 src/blixemApp/{blxFetch.cpp => blxFetch.c}         |  23 ++---
 src/blixemApp/{blxFetchDb.cpp => blxFetchDb.c}     |   6 +-
 src/blixemApp/{blxdotter.cpp => blxdotter.c}       |  23 +++--
 src/blixemApp/{blxdotter.hpp => blxdotter.h}       |   2 +-
 src/blixemApp/{blxmain.cpp => blxmain.c}           |   8 +-
 src/blixemApp/{blxview.cpp => blxview.c}           |  20 ++--
 src/blixemApp/{blxview.hpp => blxview.h}           |   0
 src/blixemApp/{blxwindow.cpp => blxwindow.c}       |  28 +++---
 src/blixemApp/{blxwindow.hpp => blxwindow.h}       |   4 +-
 src/blixemApp/{coverageview.cpp => coverageview.c} |   8 +-
 src/blixemApp/{coverageview.hpp => coverageview.h} |   2 +-
 src/blixemApp/{detailview.cpp => detailview.c}     |  14 +--
 src/blixemApp/{detailview.hpp => detailview.h}     |   4 +-
 .../{detailviewtree.cpp => detailviewtree.c}       |  14 +--
 .../{detailviewtree.hpp => detailviewtree.h}       |   6 +-
 src/blixemApp/{exonview.cpp => exonview.c}         |  16 ++--
 src/blixemApp/{exonview.hpp => exonview.h}         |   2 +-
 ...encecellrenderer.cpp => sequencecellrenderer.c} |  14 +--
 ...encecellrenderer.hpp => sequencecellrenderer.h} |   2 +-
 src/configure.ac                                   |  11 +--
 src/doc/Makefile.am                                |   8 --
 src/doc/User_doc/Makefile.am                       |  22 -----
 src/dotterApp/Makefile.am                          |  23 -----
 .../{alignmenttool.cpp => alignmenttool.c}         |   4 +-
 src/dotterApp/{dotplot.cpp => dotplot.c}           |   6 +-
 src/dotterApp/{dotter.cpp => dotter.c}             |  18 ++--
 src/dotterApp/{dotter.hpp => dotter.h}             |   2 +-
 src/dotterApp/{dotterKarlin.cpp => dotterKarlin.c} |   2 +-
 src/dotterApp/{dotterMain.cpp => dotterMain.c}     |  13 ++-
 src/dotterApp/{dotter_.hpp => dotter_.h}           |   4 +-
 src/dotterApp/{greyramptool.cpp => greyramptool.c} |   4 +-
 .../{seqtoolsExonView.cpp => seqtoolsExonView.c}   |   6 +-
 .../{seqtoolsExonView.hpp => seqtoolsExonView.h}   |   4 +-
 src/examples/Makefile.am                           |   8 --
 src/libpfetch/Makefile.am                          |  50 ----------
 src/libpfetch/libcurlobject.h                      |   9 +-
 src/libpfetch/libcurlobject_I.h                    |  10 --
 src/libpfetch/libpfetch-cmarshal.h                 |   7 --
 src/libpfetch/libpfetch.h                          |   8 --
 src/libpfetch/libpfetch_I.h                        |   8 --
 src/libpfetch/libpfetch_P.h                        |   8 --
 src/seqtoolsUtils/Makefile.am                      |  14 ---
 .../{blxGff3Parser.cpp => blxGff3Parser.c}         |   8 +-
 .../{blxGff3Parser.hpp => blxGff3Parser.h}         |   2 +-
 src/seqtoolsUtils/{blxmsp.cpp => blxmsp.c}         |   6 +-
 src/seqtoolsUtils/{blxmsp.hpp => blxmsp.h}         |   2 +-
 src/seqtoolsUtils/{blxparser.cpp => blxparser.c}   |  16 ++--
 src/seqtoolsUtils/{blxparser.hpp => blxparser.h}   |   0
 src/seqtoolsUtils/{iupac.hpp => iupac.h}           |   0
 ...seqtoolsWebBrowser.cpp => seqtoolsWebBrowser.c} |   2 +-
 src/seqtoolsUtils/{translate.cpp => translate.c}   |   4 +-
 src/seqtoolsUtils/{utilities.cpp => utilities.c}   |   2 +-
 src/seqtoolsUtils/{utilities.hpp => utilities.h}   |   1 +
 src/seqtoolsUtils/{version.hpp => version.h}       |   0
 src/test/Makefile.am                               |   8 --
 74 files changed, 305 insertions(+), 476 deletions(-)

2015-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Fix missing docs installation - BUILD"
 src/Makefile.am | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2015-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Fix installation of docs in dist file - BUILD"
 src/configure.ac                         |  4 ----
 src/doc/Design_notes/Makefile.am         | 13 -------------
 src/doc/Design_notes/modules/Makefile.am | 13 -------------
 src/doc/Makefile.am                      |  2 +-
 4 files changed, 1 insertion(+), 31 deletions(-)

2015-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Make organism abbreviation longer to avoid duplicates - RT 456864
 src/blixemApp/blixem_.hpp |  2 +-
 src/blixemApp/blxview.cpp | 30 +++++++++++++++++++++++++++++-
 2 files changed, 30 insertions(+), 2 deletions(-)

2015-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Make organism abbreviation longer to avoid duplicates - RT 456864
 src/blixemApp/blixem_.hpp |  2 +-
 src/blixemApp/blxview.cpp | 30 +++++++++++++++++++++++++++++-
 2 files changed, 30 insertions(+), 2 deletions(-)

2015-03-12  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.32.1-30-g3f48 - Update RT and git commit reports
 src/ChangeLog                                  | 536 ++++++++++++++++++-------
 src/build/release_docs/GIT_COMMITS.txt         |  20 +-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  32 +-
 3 files changed, 389 insertions(+), 199 deletions(-)

2015-03-12  Steve Miller  <sm23@sanger.ac.uk>
 editing of release notes - BUILD
 src/doc/User_doc/release_notes.html | 8 ++++++++
 1 file changed, 8 insertions(+)

2015-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix for changed library function name - TRIVIAL
 src/belvuApp/belvuConsPlot.cpp  | 2 +-
 src/belvuApp/belvuTree.cpp      | 2 +-
 src/belvuApp/belvuWindow.cpp    | 8 ++++----
 src/blixemApp/blxdotter.cpp     | 2 +-
 src/blixemApp/blxwindow.cpp     | 6 +++---
 src/dotterApp/dotter.cpp        | 2 +-
 src/seqtoolsUtils/utilities.cpp | 2 +-
 7 files changed, 12 insertions(+), 12 deletions(-)

2015-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Use gbtools monitor size code - NEW FEATURE 'gbtools'
 src/belvuApp/belvuConsPlot.cpp  |  3 +-
 src/belvuApp/belvuTree.cpp      |  3 +-
 src/belvuApp/belvuWindow.cpp    | 13 ++++----
 src/blixemApp/blxdotter.cpp     |  3 +-
 src/blixemApp/blxwindow.cpp     |  9 +++---
 src/dotterApp/dotter.cpp        |  3 +-
 src/seqtoolsUtils/utilities.cpp | 67 ++---------------------------------------
 src/seqtoolsUtils/utilities.hpp |  3 --
 8 files changed, 22 insertions(+), 82 deletions(-)

2015-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Add gitignore file for build directory - BUILD
 src/build/.gitignore | 3 +++
 1 file changed, 3 insertions(+)

2015-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 gbtools now compiles ok into seqtools - NEW FEATURE 'gbtools'
 src/belvuApp/Makefile.am      | 2 +-
 src/blixemApp/Makefile.am     | 8 ++++----
 src/seqtoolsUtils/Makefile.am | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

2015-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Minor improvement to dotter libs - BUILD
 src/dotterApp/Makefile.am | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/gbtools
2015-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix installation of docs in dist file - BUILD
 src/configure.ac                         |  4 ++++
 src/doc/Design_notes/Makefile.am         | 13 +++++++++++++
 src/doc/Design_notes/modules/Makefile.am | 13 +++++++++++++
 src/doc/Makefile.am                      |  2 +-
 4 files changed, 31 insertions(+), 1 deletion(-)

2015-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix missing docs installation - BUILD
 src/Makefile.am | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2015-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Add gitignore file for gbtools dir - BUILD
 src/gbtools/.gitignore | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

2015-03-06  Gemma Barson  <gb10@sanger.ac.uk>
 Minor change to runconfig script - BUILD
 src/runconfig.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

2015-03-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fixes to autotools files for gbtools subdir
 src/Makefile.am               | 13 +++++++++----
 src/belvuApp/Makefile.am      |  6 +++---
 src/blixemApp/Makefile.am     |  8 ++++----
 src/configure.ac              | 10 ++++++++++
 src/dotterApp/Makefile.am     |  6 +++---
 src/runconfig.sh              |  6 +++---
 src/seqtoolsUtils/Makefile.am |  8 ++++----
 7 files changed, 36 insertions(+), 21 deletions(-)

2015-03-04  Gemma Barson  <gb10@sanger.ac.uk>
 "Tidying - TRIVIAL"
 src/belvuApp/Makefile.am  |  7 +++----
 src/blixemApp/Makefile.am | 16 ++++++++--------
 src/dotterApp/Makefile.am |  3 +--
 3 files changed, 12 insertions(+), 14 deletions(-)

2015-03-04  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/cpp' into develop
2015-03-04  Gemma Barson  <gb10@sanger.ac.uk>
 "Fix error using abstract type - TRIVIAL"
 src/blixemApp/sequencecellrenderer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Fix c++ compiler errors - BUILD"
 src/belvuApp/belvu.cpp    | 3 +--
 src/blixemApp/blxview.cpp | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Fix c++ compiler errors - BUILD"
 src/belvuApp/belvu.cpp       | 6 +++++-
 src/dotterApp/dotterMain.cpp | 3 ++-
 2 files changed, 7 insertions(+), 2 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Fix more c++ compiler errors on linux - BUILD"
 src/belvuApp/belvu.cpp     | 7 ++++---
 src/blixemApp/blxFetch.cpp | 2 +-
 src/blixemApp/blxview.cpp  | 2 +-
 src/dotterApp/dotplot.cpp  | 2 +-
 4 files changed, 7 insertions(+), 6 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Fix compile error on linux - BUILD"
 src/seqtoolsUtils/blxparser.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Fix c++ compiler warnings - BUILD"
 src/belvuApp/belvuAlignment.cpp |  4 ++--
 src/blixemApp/blxFetch.cpp      | 13 +++++++++----
 src/blixemApp/blxdotter.cpp     |  4 ++--
 src/blixemApp/blxwindow.cpp     |  6 +++---
 src/seqtoolsUtils/blxmsp.cpp    |  2 +-
 src/seqtoolsUtils/blxparser.cpp |  4 ++--
 6 files changed, 19 insertions(+), 14 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Fix compiler errors - BUILD"
 src/belvuApp/belvuAlignment.cpp |  4 ++--
 src/belvuApp/belvuConsPlot.cpp  |  6 +++---
 src/belvuApp/belvuConsPlot.hpp  |  2 +-
 src/belvuApp/belvuMain.cpp      | 10 +++++-----
 src/belvuApp/belvuTree.cpp      |  6 +++---
 src/belvuApp/belvuWindow.cpp    | 10 +++++-----
 src/belvuApp/belvu_.hpp         |  6 +++---
 7 files changed, 22 insertions(+), 22 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Add C linkage to libpfetch c files - BUILD"
 src/libpfetch/libcurlobject.h      |  9 ++++++++-
 src/libpfetch/libcurlobject_I.h    | 10 ++++++++++
 src/libpfetch/libpfetch-cmarshal.h |  7 +++++++
 src/libpfetch/libpfetch.h          |  8 ++++++++
 src/libpfetch/libpfetch_I.h        |  8 ++++++++
 src/libpfetch/libpfetch_P.h        |  8 ++++++++
 6 files changed, 49 insertions(+), 1 deletion(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Fix cpp compiler errors - BUILD"
 src/belvuApp/Makefile.am                 |  4 ++--
 src/belvuApp/belvu.cpp                   | 10 +++++-----
 src/belvuApp/belvuAlignment.hpp          |  2 +-
 src/belvuApp/belvuTree.hpp               |  2 +-
 src/belvuApp/belvuWindow.hpp             |  2 +-
 src/blixemApp/Makefile.am                |  4 ++--
 src/blixemApp/bigpicture.cpp             | 12 ++++++------
 src/blixemApp/bigpicture.hpp             |  6 +++---
 src/blixemApp/bigpicturegrid.cpp         | 12 ++++++------
 src/blixemApp/bigpicturegrid.hpp         |  4 ++--
 src/blixemApp/blixem_.hpp                |  6 +++---
 src/blixemApp/blxFetch.cpp               |  8 ++++----
 src/blixemApp/blxFetchDb.cpp             |  6 +++---
 src/blixemApp/blxdotter.cpp              | 19 ++++++++++---------
 src/blixemApp/blxdotter.hpp              |  2 +-
 src/blixemApp/blxmain.cpp                |  8 ++++----
 src/blixemApp/blxview.cpp                | 16 ++++++++--------
 src/blixemApp/blxwindow.cpp              | 22 +++++++++++-----------
 src/blixemApp/blxwindow.hpp              |  4 ++--
 src/blixemApp/coverageview.cpp           |  8 ++++----
 src/blixemApp/coverageview.hpp           |  2 +-
 src/blixemApp/detailview.cpp             | 14 +++++++-------
 src/blixemApp/detailview.hpp             |  4 ++--
 src/blixemApp/detailviewtree.cpp         | 14 +++++++-------
 src/blixemApp/detailviewtree.hpp         |  6 +++---
 src/blixemApp/exonview.cpp               | 16 ++++++++--------
 src/blixemApp/exonview.hpp               |  2 +-
 src/blixemApp/sequencecellrenderer.cpp   | 14 +++++++-------
 src/blixemApp/sequencecellrenderer.hpp   |  2 +-
 src/configure.ac                         |  2 +-
 src/dotterApp/Makefile.am                |  4 ++--
 src/dotterApp/alignmenttool.cpp          |  4 ++--
 src/dotterApp/dotplot.cpp                |  4 ++--
 src/dotterApp/dotter.cpp                 | 18 +++++++++---------
 src/dotterApp/dotter.hpp                 |  2 +-
 src/dotterApp/dotterKarlin.cpp           |  2 +-
 src/dotterApp/dotterMain.cpp             | 10 +++++-----
 src/dotterApp/dotter_.hpp                |  4 ++--
 src/dotterApp/greyramptool.cpp           |  4 ++--
 src/dotterApp/seqtoolsExonView.cpp       |  6 +++---
 src/dotterApp/seqtoolsExonView.hpp       |  4 ++--
 src/seqtoolsUtils/Makefile.am            |  6 +++---
 src/seqtoolsUtils/blxGff3Parser.cpp      |  8 ++++----
 src/seqtoolsUtils/blxGff3Parser.hpp      |  2 +-
 src/seqtoolsUtils/blxmsp.cpp             |  4 ++--
 src/seqtoolsUtils/blxmsp.hpp             |  2 +-
 src/seqtoolsUtils/blxparser.cpp          |  8 ++++----
 src/seqtoolsUtils/seqtoolsWebBrowser.cpp |  2 +-
 src/seqtoolsUtils/translate.cpp          |  4 ++--
 src/seqtoolsUtils/utilities.cpp          |  2 +-
 50 files changed, 167 insertions(+), 166 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Change libpfetch files back to .h/.c - BUILD"
 src/libpfetch/{libcurlobject.cpp => libcurlobject.c}           | 0
 src/libpfetch/{libpfetch-cmarshal.cpp => libpfetch-cmarshal.c} | 0
 src/libpfetch/{libpfetch-utils.cpp => libpfetch-utils.c}       | 0
 src/libpfetch/{libpfetch.cpp => libpfetch.c}                   | 0
 src/libpfetch/{libpfetch_I.hpp => libpfetch_I.h}               | 0
 src/libpfetch/{libpfetch_P.hpp => libpfetch_P.h}               | 0
 6 files changed, 0 insertions(+), 0 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Rename .h files to .hpp - BUILD"
 src/belvuApp/{belvuAlignment.h => belvuAlignment.hpp}              | 0
 src/belvuApp/{belvuConsPlot.h => belvuConsPlot.hpp}                | 0
 src/belvuApp/{belvuTree.h => belvuTree.hpp}                        | 0
 src/belvuApp/{belvuWindow.h => belvuWindow.hpp}                    | 0
 src/belvuApp/{belvu_.h => belvu_.hpp}                              | 0
 src/blixemApp/{bigpicture.h => bigpicture.hpp}                     | 0
 src/blixemApp/{bigpicturegrid.h => bigpicturegrid.hpp}             | 0
 src/blixemApp/{blixem_.h => blixem_.hpp}                           | 0
 src/blixemApp/{blxdotter.h => blxdotter.hpp}                       | 0
 src/blixemApp/{blxview.h => blxview.hpp}                           | 0
 src/blixemApp/{blxwindow.h => blxwindow.hpp}                       | 0
 src/blixemApp/{coverageview.h => coverageview.hpp}                 | 0
 src/blixemApp/{detailview.h => detailview.hpp}                     | 0
 src/blixemApp/{detailviewtree.h => detailviewtree.hpp}             | 0
 src/blixemApp/{exonview.h => exonview.hpp}                         | 0
 src/blixemApp/{sequencecellrenderer.h => sequencecellrenderer.hpp} | 0
 src/dotterApp/{dotter.h => dotter.hpp}                             | 0
 src/dotterApp/{dotter_.h => dotter_.hpp}                           | 0
 src/dotterApp/{seqtoolsExonView.h => seqtoolsExonView.hpp}         | 0
 src/libpfetch/{libpfetch_I.h => libpfetch_I.hpp}                   | 0
 src/libpfetch/{libpfetch_P.h => libpfetch_P.hpp}                   | 0
 src/seqtoolsUtils/{blxGff3Parser.h => blxGff3Parser.hpp}           | 0
 src/seqtoolsUtils/{blxmsp.h => blxmsp.hpp}                         | 0
 src/seqtoolsUtils/{blxparser.h => blxparser.hpp}                   | 0
 src/seqtoolsUtils/{iupac.h => iupac.hpp}                           | 0
 src/seqtoolsUtils/{utilities.h => utilities.hpp}                   | 0
 src/seqtoolsUtils/{version.h => version.hpp}                       | 0
 27 files changed, 0 insertions(+), 0 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Renmae .c files to .cpp - BUILD"
 src/belvuApp/{belvu.c => belvu.cpp}                                | 0
 src/belvuApp/{belvuAlignment.c => belvuAlignment.cpp}              | 0
 src/belvuApp/{belvuConsPlot.c => belvuConsPlot.cpp}                | 0
 src/belvuApp/{belvuMain.c => belvuMain.cpp}                        | 0
 src/belvuApp/{belvuTree.c => belvuTree.cpp}                        | 0
 src/belvuApp/{belvuWindow.c => belvuWindow.cpp}                    | 0
 src/blixemApp/{bigpicture.c => bigpicture.cpp}                     | 0
 src/blixemApp/{bigpicturegrid.c => bigpicturegrid.cpp}             | 0
 src/blixemApp/{blxFetch.c => blxFetch.cpp}                         | 0
 src/blixemApp/{blxFetchDb.c => blxFetchDb.cpp}                     | 0
 src/blixemApp/{blxdotter.c => blxdotter.cpp}                       | 0
 src/blixemApp/{blxmain.c => blxmain.cpp}                           | 0
 src/blixemApp/{blxview.c => blxview.cpp}                           | 0
 src/blixemApp/{blxwindow.c => blxwindow.cpp}                       | 0
 src/blixemApp/{coverageview.c => coverageview.cpp}                 | 0
 src/blixemApp/{detailview.c => detailview.cpp}                     | 0
 src/blixemApp/{detailviewtree.c => detailviewtree.cpp}             | 0
 src/blixemApp/{exonview.c => exonview.cpp}                         | 0
 src/blixemApp/{sequencecellrenderer.c => sequencecellrenderer.cpp} | 0
 src/dotterApp/{alignmenttool.c => alignmenttool.cpp}               | 0
 src/dotterApp/{dotplot.c => dotplot.cpp}                           | 0
 src/dotterApp/{dotter.c => dotter.cpp}                             | 0
 src/dotterApp/{dotterKarlin.c => dotterKarlin.cpp}                 | 0
 src/dotterApp/{dotterMain.c => dotterMain.cpp}                     | 0
 src/dotterApp/{greyramptool.c => greyramptool.cpp}                 | 0
 src/dotterApp/{seqtoolsExonView.c => seqtoolsExonView.cpp}         | 0
 src/libpfetch/{libcurlobject.c => libcurlobject.cpp}               | 0
 src/libpfetch/{libpfetch-cmarshal.c => libpfetch-cmarshal.cpp}     | 0
 src/libpfetch/{libpfetch-utils.c => libpfetch-utils.cpp}           | 0
 src/libpfetch/{libpfetch.c => libpfetch.cpp}                       | 0
 src/seqtoolsUtils/{blxGff3Parser.c => blxGff3Parser.cpp}           | 0
 src/seqtoolsUtils/{blxmsp.c => blxmsp.cpp}                         | 0
 src/seqtoolsUtils/{blxparser.c => blxparser.cpp}                   | 0
 src/seqtoolsUtils/{seqtoolsWebBrowser.c => seqtoolsWebBrowser.cpp} | 0
 src/seqtoolsUtils/{translate.c => translate.cpp}                   | 0
 src/seqtoolsUtils/{utilities.c => utilities.cpp}                   | 0
 36 files changed, 0 insertions(+), 0 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Remove debug output - TRIVIAL"
 src/seqtoolsUtils/utilities.h | 1 -
 1 file changed, 1 deletion(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "Finish moving autotools stuff to subdirs - BUILD"
 src/belvuApp/Makefile.am      | 4 ++--
 src/blixemApp/Makefile.am     | 4 ++--
 src/dotterApp/Makefile.am     | 4 ++--
 src/libpfetch/Makefile.am     | 2 +-
 src/seqtoolsUtils/Makefile.am | 2 +-
 5 files changed, 8 insertions(+), 8 deletions(-)

2015-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 "WIP: change autotools to use subdirs - BUILD"
 src/Makefile.am               | 103 ++----------------------------------------
 src/belvuApp/Makefile.am      |  23 ++++++++++
 src/blixemApp/Makefile.am     |  45 ++++++++++++++++++
 src/configure.ac              |   9 +++-
 src/doc/Makefile.am           |   8 ++++
 src/doc/User_doc/Makefile.am  |  22 +++++++++
 src/dotterApp/Makefile.am     |  23 ++++++++++
 src/examples/Makefile.am      |   8 ++++
 src/libpfetch/Makefile.am     |  50 ++++++++++++++++++++
 src/seqtoolsUtils/Makefile.am |  14 ++++++
 src/test/Makefile.am          |   8 ++++
 11 files changed, 213 insertions(+), 100 deletions(-)

2015-02-18  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/multi_dotter' into develop
2015-02-18  Gemma Barson  <gb10@sanger.ac.uk>
 Start multiple dotters from blixem
 src/blixemApp/blxdotter.c     | 130 ++++++++++++++++++++++++++++--------------
 src/blixemApp/blxdotter.h     |   2 +-
 src/blixemApp/blxview.c       |   2 +-
 src/blixemApp/blxwindow.c     |  18 ++++--
 src/blixemApp/blxwindow.h     |   2 +-
 src/blixemApp/detailview.c    |   2 +-
 src/seqtoolsUtils/utilities.h |   2 +
 7 files changed, 108 insertions(+), 50 deletions(-)

2015-02-17  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-02-17  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'hotfix/4.32.1' into production
2015-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fix regression caused by previous change
 src/blixemApp/blxwindow.c | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

2015-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Efficiency improvements starting up blixem
 src/blixemApp/blxwindow.c  | 5 +++--
 src/seqtoolsUtils/blxmsp.c | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

2015-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fix regression caused by previous change
 src/blixemApp/blxwindow.c | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

2015-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Efficiency improvements starting up blixem
 src/blixemApp/blxwindow.c  | 5 +++--
 src/seqtoolsUtils/blxmsp.c | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

2015-01-29  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2015-01-29  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.32' into production
2015-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fix compiler warnings for unused variables
 src/blixemApp/blxdotter.c     | 12 ------------
 src/dotterApp/dotterMain.c    |  4 +---
 src/libpfetch/libpfetch.c     | 20 ++++++++------------
 src/seqtoolsUtils/blxparser.c | 29 -----------------------------
 4 files changed, 9 insertions(+), 56 deletions(-)

2015-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 Minor change to future-proof gtk version checks
 src/belvuApp/belvuWindow.c    | 2 +-
 src/blixemApp/blxwindow.c     | 6 +++---
 src/dotterApp/dotter.c        | 2 +-
 src/seqtoolsUtils/utilities.c | 4 ++--
 src/seqtoolsUtils/utilities.h | 4 ++++
 5 files changed, 11 insertions(+), 7 deletions(-)

2015-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fix compile error on older versions of GTK
 src/seqtoolsUtils/utilities.c | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

2015-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fix belvu bug where windows appear on wrong monitor
 src/belvuApp/belvuConsPlot.c |  5 -----
 src/belvuApp/belvuTree.c     |  5 -----
 src/belvuApp/belvuWindow.c   | 10 ----------
 3 files changed, 20 deletions(-)

2015-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fix window sizes on dual monitors
 src/belvuApp/belvuConsPlot.c  |  5 ++--
 src/belvuApp/belvuTree.c      |  5 ++--
 src/belvuApp/belvuWindow.c    | 26 ++++++++----------
 src/blixemApp/blxdotter.c     |  6 ++--
 src/blixemApp/blxwindow.c     | 17 ++++++------
 src/dotterApp/dotter.c        |  5 ++--
 src/seqtoolsUtils/utilities.c | 64 +++++++++++++++++++++++++++++++++++++------
 src/seqtoolsUtils/utilities.h |  3 +-
 8 files changed, 86 insertions(+), 45 deletions(-)

2015-01-23  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.31-31-gd010 - Update RT and git commit reports
 src/ChangeLog | 6 ++++++
 1 file changed, 6 insertions(+)

2015-01-23  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.31-30-g890b - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

2015-01-21  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.31-29-g75f3 - Update RT and git commit reports
 src/ChangeLog                                  | 15 +++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 17 insertions(+), 1 deletion(-)

2015-01-21  Gemma Barson  <gb10@sanger.ac.uk>
 Fix potential crash in blixem
 src/blixemApp/detailview.c | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

2015-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes
 src/doc/User_doc/release_notes.html | 1 +
 1 file changed, 1 insertion(+)

2015-01-13  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.31-26-g476d - Update RT and git commit reports
 src/ChangeLog | 7 +++++++
 1 file changed, 7 insertions(+)

2015-01-13  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.31-25-gfcf4 - Update RT and git commit reports
 src/ChangeLog                                  | 176 ++++++++++++-------------
 src/build/release_docs/GIT_COMMITS.txt         |  15 ++-
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |   2 +-
 3 files changed, 96 insertions(+), 97 deletions(-)

2015-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Minor update to blixem quick start guide
 src/doc/User_doc/blixem_quick_start.html | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2015-01-05  Ed Griffiths  <edgrif@sanger.ac.uk>
 "add doc required by Sanger software policy."
 src/RANGE_OF_YEARS_COPYRIGHT | 9 +++++++++
 1 file changed, 9 insertions(+)

2014-12-18  Ed Griffiths  <edgrif@sanger.ac.uk>
 "add in X11 and m libs to link, otherwise not found on 64 bit ubuntu."
 src/Makefile.am | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

2014-12-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug where matches can be treated like basic features
 src/seqtoolsUtils/blxGff3Parser.c | 59 ++++++++++++++++++++-------------------
 src/seqtoolsUtils/blxmsp.h        |  3 +-
 2 files changed, 33 insertions(+), 29 deletions(-)

2014-11-28  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'production' into develop
2014-11-28  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'release/4.31' into production
2014-11-27  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.30-23-g232f - Update RT and git commit reports
 src/ChangeLog                                  | 12 ++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         | 15 +--------------
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 14 insertions(+), 15 deletions(-)

2014-11-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug where styles were not being picked up for new features
 src/blixemApp/blxwindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-11-27  Gemma Barson  <gb10@sanger.ac.uk>
 Set NULL SO ID for invalid Sequence type
 src/seqtoolsUtils/blxGff3Parser.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

2014-11-27  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.31' into develop
2014-11-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fix problem with drag-and-drop of 'Sequence' features from ZMap (RT436929)
 src/seqtoolsUtils/blxGff3Parser.c | 4 ++++
 1 file changed, 4 insertions(+)

2014-11-26  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.30-21-g89cc - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/GIT_COMMITS.txt         | 1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 3 files changed, 9 insertions(+), 1 deletion(-)

2014-11-25  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.30-20-g15bb - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/GIT_COMMITS.txt         | 1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 3 files changed, 9 insertions(+), 1 deletion(-)

2014-11-24  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.30-19-gdf004 - Update RT and git commit reports
 src/ChangeLog                                  | 38 ++++++++++++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  2 ++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 41 insertions(+), 1 deletion(-)

2014-11-24  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.31' into develop
2014-11-24  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/basic_features' into release/4.31
2014-11-24  Gemma Barson  <gb10@sanger.ac.uk>
 Update blixem usage info to reflect support for basic types
 src/blixemApp/blxmain.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2014-11-21  Gemma Barson  <gb10@sanger.ac.uk>
 Improve display of exons and basic features in the detail view
 src/blixemApp/sequencecellrenderer.c | 51 ++++++++++--------------------------
 1 file changed, 14 insertions(+), 37 deletions(-)

2014-11-21  Gemma Barson  <gb10@sanger.ac.uk>
 Implement basic feature type properly
 src/blixemApp/blxview.c              |   2 +-
 src/blixemApp/blxwindow.c            |   2 +-
 src/blixemApp/detailview.c           |  17 +++---
 src/blixemApp/detailviewtree.c       |  20 +++++--
 src/blixemApp/exonview.c             |   6 +-
 src/blixemApp/exonview.h             |   6 +-
 src/blixemApp/sequencecellrenderer.c |  40 ++++++++-----
 src/dotterApp/seqtoolsExonView.c     |   6 +-
 src/seqtoolsUtils/blxmsp.c           | 112 ++++++++++++++++++++++-------------
 src/seqtoolsUtils/blxmsp.h           |  11 ++--
 10 files changed, 136 insertions(+), 86 deletions(-)

2014-11-21  Gemma Barson  <gb10@sanger.ac.uk>
 Quick hack to support basic feature types using exon code
 src/seqtoolsUtils/blxGff3Parser.c | 4 +++-
 src/seqtoolsUtils/blxmsp.h        | 5 +++++
 2 files changed, 8 insertions(+), 1 deletion(-)

2014-11-24  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/basic_features' into develop
2014-11-24  Gemma Barson  <gb10@sanger.ac.uk>
 Update blixem usage info to reflect support for basic types
 src/blixemApp/blxmain.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2014-11-24  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes
 src/doc/User_doc/release_notes.html | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

2014-11-21  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/basic_features' into develop
2014-11-21  Gemma Barson  <gb10@sanger.ac.uk>
 Improve display of exons and basic features in the detail view
 src/blixemApp/sequencecellrenderer.c | 51 ++++++++++--------------------------
 1 file changed, 14 insertions(+), 37 deletions(-)

2014-11-21  Gemma Barson  <gb10@sanger.ac.uk>
 Implement basic feature type properly
 src/blixemApp/blxview.c              |   2 +-
 src/blixemApp/blxwindow.c            |   2 +-
 src/blixemApp/detailview.c           |  17 +++---
 src/blixemApp/detailviewtree.c       |  20 +++++--
 src/blixemApp/exonview.c             |   6 +-
 src/blixemApp/exonview.h             |   6 +-
 src/blixemApp/sequencecellrenderer.c |  40 ++++++++-----
 src/dotterApp/seqtoolsExonView.c     |   6 +-
 src/seqtoolsUtils/blxmsp.c           | 112 ++++++++++++++++++++++-------------
 src/seqtoolsUtils/blxmsp.h           |  11 ++--
 10 files changed, 136 insertions(+), 86 deletions(-)

2014-11-21  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.30-13-g3ab2 - Update RT and git commit reports
 src/ChangeLog                          | 7 +++++++
 src/build/release_docs/GIT_COMMITS.txt | 1 +
 2 files changed, 8 insertions(+)

2014-11-21  Gemma Barson  <gb10@sanger.ac.uk>
 Quick hack to support basic feature types using exon code
 src/seqtoolsUtils/blxGff3Parser.c | 4 +++-
 src/seqtoolsUtils/blxmsp.h        | 5 +++++
 2 files changed, 8 insertions(+), 1 deletion(-)

2014-11-21  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.30-12-g5b4f - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/GIT_COMMITS.txt         | 1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 3 files changed, 9 insertions(+), 1 deletion(-)

2014-11-19  Ed Griffiths  <edgrif@sanger.ac.uk>
 update INSTALL files to match Gemma's web writeups.
 src/INSTALL         | 436 +++++++++++++++++++++++++++++++++++++++++++---------
 src/INSTALL.linux   |  60 ++++++++
 src/INSTALL.mac     |  51 ++++++
 src/INSTALL.windows |  81 +++++-----
 4 files changed, 513 insertions(+), 115 deletions(-)

2014-11-17  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.30-11-g7c4ef - Update RT and git commit reports
 src/ChangeLog                                  | 16 +++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  3 +++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 32 +++++++++++++++++++++++++-
 3 files changed, 50 insertions(+), 1 deletion(-)

2014-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.31' into develop
2014-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes
 src/doc/User_doc/release_notes.html | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

2014-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/GUI_improvements' into develop
2014-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Add tooltips to greyramp tool buttons
 src/dotterApp/greyramptool.c | 4 ++++
 1 file changed, 4 insertions(+)

2014-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Add maximise button for greyramp tool
 src/dotterApp/greyramptool.c | 31 ++++++++++++++++++++++++-------
 1 file changed, 24 insertions(+), 7 deletions(-)

2014-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fix keyboard shortcuts on separate tools
 src/dotterApp/dotter.c | 121 +++++++++++++++++++++++++++----------------------
 1 file changed, 66 insertions(+), 55 deletions(-)

2014-11-13  Gemma Barson  <gb10@sanger.ac.uk>
 Move tool menus to main window
 src/dotterApp/alignmenttool.c | 297 +++++++++---------------------------------
 src/dotterApp/dotter.c        | 185 ++++++++++++++++++++++----
 src/dotterApp/dotter_.h       |  10 +-
 src/dotterApp/greyramptool.c  |  76 +----------
 4 files changed, 235 insertions(+), 333 deletions(-)

2014-11-13  Gemma Barson  <gb10@sanger.ac.uk>
 Add right click option to maximise greyramp tool
 src/dotterApp/alignmenttool.c |  4 ++--
 src/dotterApp/dotter.c        | 34 ++++++++++++++++++++++++++++++++--
 src/dotterApp/greyramptool.c  |  8 ++++----
 3 files changed, 38 insertions(+), 8 deletions(-)

2014-11-13  Gemma Barson  <gb10@sanger.ac.uk>
 Trivial menu name change
 src/dotterApp/alignmenttool.c | 2 +-
 src/dotterApp/greyramptool.c  | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

2014-11-13  Steve Miller  <sm23@sanger.ac.uk>
 update of release notes for v. 4.31
 src/doc/User_doc/release_notes.html | 7 +++++++
 1 file changed, 7 insertions(+)

2014-11-12  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.30-8-g588a - Update RT and git commit reports
 src/ChangeLog                          | 7 +++++++
 src/build/release_docs/GIT_COMMITS.txt | 1 +
 2 files changed, 8 insertions(+)

2014-11-12  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.30-7-g8cf9 - Update RT and git commit reports
 src/ChangeLog                                  | 79 +++++++++-----------------
 src/build/release_docs/GIT_COMMITS.txt         | 20 +++----
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 36 insertions(+), 65 deletions(-)

2014-11-03  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'production' into develop
2014-11-03  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'release/4.30' into develop
2014-11-03  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'release/4.30' into production
2014-10-31  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.29-9-gbec7 - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/GIT_COMMITS.txt         | 1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 3 files changed, 9 insertions(+), 1 deletion(-)

2014-10-30  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.29-8-ge868 - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/GIT_COMMITS.txt         | 1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 3 files changed, 9 insertions(+), 1 deletion(-)

2014-10-29  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.29-7-gcbf0 - Update RT and git commit reports
 src/ChangeLog                                  | 7 +++++++
 src/build/release_docs/GIT_COMMITS.txt         | 1 +
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 2 +-
 3 files changed, 9 insertions(+), 1 deletion(-)

2014-10-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix typo in configure.ac causing it to fail
 src/configure.ac | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-10-27  Gemma Barson  <gb10@sanger.ac.uk>
 Update blixem quick start guide with minor colour change
 src/doc/User_doc/blixem_quick_start.html | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2014-10-23  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.29-6-gf0e18 - Update RT and git commit reports
 src/ChangeLog                                  | 12 ++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  2 ++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 15 insertions(+), 1 deletion(-)

2014-10-22  Gemma Barson  <gb10@sanger.ac.uk>
 Make sqlite optional
 src/configure.ac | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

2014-10-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fix autoconf error on cygwin
 src/Makefile.am | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

2014-10-20  Gemma Barson  <gb10@sanger.ac.uk>
 Build: remove obsolete hack to pkg-config path
 src/runconfig.sh | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

2014-10-17  Steve Miller  <sm23@sanger.ac.uk>
 creation of release notes after build
 src/doc/User_doc/release_notes.html | 11 +++++++++++
 1 file changed, 11 insertions(+)

2014-10-17  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.29-4-gd795 - Update RT and git commit reports
 src/ChangeLog                                  | 234 +++----------------------
 src/build/release_docs/GIT_COMMITS.txt         |  21 +--
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  26 +--
 3 files changed, 28 insertions(+), 253 deletions(-)

2014-10-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fix potential crash with accessing null value
 src/blixemApp/detailviewtree.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-10-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fix infinite loop loading features file
 src/blixemApp/blxview.c           | 22 ++++++++++++++++------
 src/blixemApp/blxwindow.c         |  6 +++++-
 src/seqtoolsUtils/blxGff3Parser.c |  3 ++-
 src/seqtoolsUtils/blxmsp.c        | 34 ++++++++++++++++++++++------------
 src/seqtoolsUtils/blxmsp.h        |  4 ++--
 src/seqtoolsUtils/blxparser.c     | 12 ++++++------
 6 files changed, 53 insertions(+), 28 deletions(-)

2014-10-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug reading files with carriage return chars
 src/belvuApp/belvu.c | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

2014-09-30  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2014-09-30  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.29' into production
2014-09-18  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.28-41-ga22f - Update RT and git commit reports
 src/ChangeLog                                  | 12 ++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  3 +++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  2 +-
 3 files changed, 16 insertions(+), 1 deletion(-)

2014-09-15  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes for 4.29
 src/doc/User_doc/release_notes.html | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

2014-09-15  zmap  <zmap@sanger.ac.uk>
 SeqTools version 4.28-39-gf6e3 - Update RT and git commit reports
 src/ChangeLog                                  | 200 +++++++++++++++++++++++++
 src/build/release_docs/GIT_COMMITS.txt         |  19 +++
 src/build/release_docs/RT_TICKETS_RESOLVED.txt |  30 ++++
 3 files changed, 249 insertions(+)

2014-09-15  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dotter_transcript' into develop
2014-09-15  Gemma Barson  <gb10@sanger.ac.uk>
 Dotter ref vs itself now uses big picture range
 src/blixemApp/blxdotter.c | 42 +-----------------------------------------
 1 file changed, 1 insertion(+), 41 deletions(-)

2014-09-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fix minor issues with dotter dialog updates
 src/blixemApp/blxdotter.c | 85 ++++++++++++++++++++++++-----------------------
 1 file changed, 44 insertions(+), 41 deletions(-)

2014-09-15  Gemma Barson  <gb10@sanger.ac.uk>
 Tidying: reorganise file
 src/blixemApp/blxdotter.c | 1238 +++++++++++++++++++++++----------------------
 1 file changed, 627 insertions(+), 611 deletions(-)

2014-09-15  Gemma Barson  <gb10@sanger.ac.uk>
 Tidying and improvements to dotter dialog
 src/blixemApp/blixem_.h   |   4 +-
 src/blixemApp/blxdotter.c | 350 ++++++++++++++++++++++++----------------------
 src/blixemApp/blxwindow.c |   2 +-
 3 files changed, 189 insertions(+), 167 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dotter_transcript' into develop
2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 don't reset dialog page when select seq
 src/blixemApp/blxdotter.c | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Don't reset to cached values when selecting sequence
 src/blixemApp/blxdotter.c | 49 +++++++++++++++++++++++++----------------------
 1 file changed, 26 insertions(+), 23 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Minor improvements to tooltips and window size
 src/blixemApp/blxdotter.c | 31 ++++++++++++++++++++++++++-----
 1 file changed, 26 insertions(+), 5 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/minimise_greyramp' into develop
2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Minimise greyramp tool by default
 src/dotterApp/dotter.c | 24 +++++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: minimised greyramp tool
 src/dotterApp/dotter.c       |  12 ++-
 src/dotterApp/dotter_.h      |   1 +
 src/dotterApp/greyramptool.c | 175 +++++++++++++++++++++++++++++++++++++------
 3 files changed, 162 insertions(+), 26 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dotter_transcript' into develop
2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bugs with sending transcript to dotter
 src/seqtoolsUtils/blxmsp.c | 29 ++++++++++++++++++++++++-----
 1 file changed, 24 insertions(+), 5 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Add option to sleep dotter on startup
 src/blixemApp/blixem_.h   |  1 +
 src/blixemApp/blxdotter.c | 53 +++++++++++++++++++++++++++++++++++++++++------
 src/blixemApp/blxdotter.h |  2 +-
 src/blixemApp/blxview.c   |  2 +-
 src/blixemApp/blxwindow.c |  1 +
 5 files changed, 51 insertions(+), 8 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Add sleep argument to dotter
 src/dotterApp/dotterMain.c | 9 +++++++++
 1 file changed, 9 insertions(+)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug sending transcript to dotter
 src/seqtoolsUtils/blxmsp.c | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: pass transcript to dotter
 src/blixemApp/blxdotter.c  | 42 +++++++++++++++++++------
 src/seqtoolsUtils/blxmsp.c | 77 +++++++++++++++++++++++++++++++++++++++++++---
 src/seqtoolsUtils/blxmsp.h |  1 +
 3 files changed, 106 insertions(+), 14 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dotter_transcript' into develop
2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with caching ref seq type to dotter against
 src/blixemApp/blxdotter.c | 65 +++++++++++++++++++++++------------------------
 src/blixemApp/blxdotter.h |  4 +--
 src/blixemApp/blxview.c   |  2 +-
 3 files changed, 35 insertions(+), 36 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Update dotter title with transcript name
 src/blixemApp/blxdotter.c | 92 +++++++++++++++++++++++++++++++++--------------
 src/blixemApp/blxwindow.c | 88 ++++++++++++++++++++++++++++-----------------
 src/blixemApp/blxwindow.h |  2 ++
 3 files changed, 122 insertions(+), 60 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix minor bug with cached dotter type not updating
 src/blixemApp/blxdotter.c | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Set correct dotter title for transcript
 src/blixemApp/blxdotter.c | 31 ++++++++++++++++++++++---------
 1 file changed, 22 insertions(+), 9 deletions(-)

2014-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Cache dotter-transcript setting
 src/blixemApp/blixem_.h   | 10 ++++++-
 src/blixemApp/blxdotter.c | 73 ++++++++++++++++++++++++++++++-----------------
 src/blixemApp/blxwindow.c |  8 +-----
 src/blixemApp/blxwindow.h |  1 -
 4 files changed, 57 insertions(+), 35 deletions(-)

2014-09-11  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: add facility to dotter vs transcript sequence
 src/blixemApp/blxdotter.c     | 166 ++++++++++++++++++++++++++++--------------
 src/blixemApp/blxdotter.h     |   2 +-
 src/blixemApp/blxview.c       |   2 +-
 src/blixemApp/blxwindow.c     |  56 ++++++++++++++
 src/blixemApp/blxwindow.h     |   2 +
 src/seqtoolsUtils/blxmsp.c    |  65 +++++++++++++++++
 src/seqtoolsUtils/blxmsp.h    |   2 +
 src/seqtoolsUtils/utilities.h |   1 +
 8 files changed, 241 insertions(+), 55 deletions(-)

2014-09-10  Gemma Barson  <gb10@sanger.ac.uk>
 Allow blixem to open on a fasta file only
 src/blixemApp/blxmain.c | 179 ++++++++++++++++++++++++++++++------------------
 1 file changed, 111 insertions(+), 68 deletions(-)

2014-09-04  Gemma Barson  <gb10@sanger.ac.uk>
 Remove spurious warning when dottering otf
 src/blixemApp/blxdotter.c | 16 ----------------
 1 file changed, 16 deletions(-)

2014-09-04  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dotter_otf' into develop
2014-09-04  Gemma Barson  <gb10@sanger.ac.uk>
 Tidy layout of dotter dialog
 src/blixemApp/blxdotter.c | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

2014-09-04  Gemma Barson  <gb10@sanger.ac.uk>
 Update dotter dialog title when toggle match type
 src/blixemApp/blxdotter.c | 123 ++++++++++++++++++++++++++++------------------
 1 file changed, 76 insertions(+), 47 deletions(-)

2014-09-04  Gemma Barson  <gb10@sanger.ac.uk>
 Set dotter dialog title for on-the-fly dotter
 src/blixemApp/blxdotter.c | 199 +++++++++++++++++++++++++++++++++-------------
 1 file changed, 143 insertions(+), 56 deletions(-)

2014-09-04  Gemma Barson  <gb10@sanger.ac.uk>
 Save previously-used pasted sequence
 src/blixemApp/blixem_.h   |  1 +
 src/blixemApp/blxdotter.c | 42 +++++++++++++++++++++++++++++++++++++++---
 src/blixemApp/blxwindow.c |  1 +
 3 files changed, 41 insertions(+), 3 deletions(-)

2014-09-04  Gemma Barson  <gb10@sanger.ac.uk>
 Allow user to paste fasta or raw sequence in dotter dialog
 src/blixemApp/blxdotter.c | 214 ++++++++++++++++++++++++++++++++++------------
 1 file changed, 158 insertions(+), 56 deletions(-)

2014-09-04  Gemma Barson  <gb10@sanger.ac.uk>
 Allow user to paste raw sequence to send to dotter
 src/blixemApp/blixem_.h   |  12 +-
 src/blixemApp/blxdotter.c | 540 ++++++++++++++++++++++++++++++++++------------
 src/blixemApp/blxdotter.h |   3 +-
 src/blixemApp/blxview.c   |   3 +-
 src/blixemApp/blxwindow.c |   2 +-
 5 files changed, 419 insertions(+), 141 deletions(-)

2014-09-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug with tree bootstrapping in Belvu
 src/belvuApp/belvu.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2014-09-01  Gemma Barson  <gb10@sanger.ac.uk>
 Add RT and git notes files
 src/build/release_docs/GIT_COMMITS.txt         | 0
 src/build/release_docs/RT_TICKETS_RESOLVED.txt | 0
 2 files changed, 0 insertions(+), 0 deletions(-)

2014-08-28  Gemma Barson  <gb10@sanger.ac.uk>
 Minor updates to windows installation instructions
 src/INSTALL.windows | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2014-07-28  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'production' into develop
2014-07-28  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'release/4.28' into develop
2014-07-28  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'release/4.28' into production
2014-07-11  Ed Griffiths  <edgrif@sanger.ac.uk>
 "add the original match sequence name."
 src/blixemApp/blxFetch.c          | 11 ++++++++++
 src/seqtoolsUtils/blxGff3Parser.c | 18 ++++++++++------
 src/seqtoolsUtils/blxmsp.c        | 43 +++++++++++++++++++++++++++++++--------
 src/seqtoolsUtils/blxmsp.h        | 24 +++++++++++++++-------
 src/seqtoolsUtils/blxparser.c     | 14 ++++++-------
 5 files changed, 81 insertions(+), 29 deletions(-)

2014-07-11  Ed Griffiths  <edgrif@sanger.ac.uk>
 "add -w flag for sleeping after command parsing."
 src/blixemApp/blxmain.c | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

2014-07-02  Gemma Barson  <gb10@sanger.ac.uk>
 Features now use id as name if Name tag not given
 src/seqtoolsUtils/blxmsp.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-06-30  Gemma Barson  <gb10@sanger.ac.uk>
 Present the blixem window as soon as you drag over it
 src/blixemApp/blxwindow.c | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

2014-06-30  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug where alignment tool coord is not in correct position
 src/dotterApp/alignmenttool.c | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

2014-06-27  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2014-06-27  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.27' into production
2014-06-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fix simple sorting bug which caused refiltering to stop working
 src/seqtoolsUtils/blxmsp.c | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

2014-06-23  Gemma Barson  <gb10@sanger.ac.uk>
 Improve the way that dotter clears up the tool windows
 src/dotterApp/dotter.c | 41 +++++++++++++++++++++--------------------
 1 file changed, 21 insertions(+), 20 deletions(-)

2014-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.27' into develop
2014-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fix potential double destroy of tool windows
 src/blixemApp/blxmain.c    |  3 ++-
 src/dotterApp/dotter.c     | 12 ++++++------
 src/dotterApp/dotterMain.c |  3 ++-
 3 files changed, 10 insertions(+), 8 deletions(-)

2014-06-16  Gemma Barson  <gb10@sanger.ac.uk>
 Avoid crash if feature name is not set
 src/blixemApp/detailviewtree.c | 3 +++
 src/seqtoolsUtils/blxmsp.c     | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

2014-06-16  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/paper' into develop
2014-06-16  Gemma Barson  <gb10@sanger.ac.uk>
 Scale images so looks ok at 170mm width
 src/doc/Publications/bmc_paper/fig1_blixem.png     | Bin 233664 -> 103031 bytes
 src/doc/Publications/bmc_paper/fig2_dotter.png     | Bin 82269 -> 63536 bytes
 .../bmc_paper/fig3_belvu_conservation.png          | Bin 131393 -> 122860 bytes
 .../Publications/bmc_paper/fig4_belvu_residues.png | Bin 122186 -> 113290 bytes
 src/doc/Publications/bmc_paper/fig5_belvu_plot.png | Bin 24498 -> 28759 bytes
 src/doc/Publications/bmc_paper/fig6_belvu_tree.png | Bin 86198 -> 77644 bytes
 6 files changed, 0 insertions(+), 0 deletions(-)

2014-06-16  Gemma Barson  <gb10@sanger.ac.uk>
 Add cover letter
 src/doc/Publications/bmc_paper/cover_letter.txt | 4 ++++
 1 file changed, 4 insertions(+)

2014-06-16  Gemma Barson  <gb10@sanger.ac.uk>
 Add competing interests
 src/doc/Publications/bmc_paper/seqtools.tex | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

2014-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 Update figures and seqtools version
 src/doc/Publications/bmc_paper/fig1_blixem.jpg | Bin 687871 -> 0 bytes
 src/doc/Publications/bmc_paper/fig1_blixem.png | Bin 0 -> 233664 bytes
 src/doc/Publications/bmc_paper/fig2_dotter.jpg | Bin 358328 -> 0 bytes
 src/doc/Publications/bmc_paper/fig2_dotter.png | Bin 0 -> 82269 bytes
 src/doc/Publications/bmc_paper/seqtools.tex    |   4 ++--
 5 files changed, 2 insertions(+), 2 deletions(-)

2014-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 First draft of BMC paper
 .gitignore                                         |    5 +
 src/doc/Publications/bmc_paper/bmc_article.bst     | 1880 ++++++++++++++++++++
 src/doc/Publications/bmc_paper/bmc_article.cls     |  138 ++
 src/doc/Publications/bmc_paper/fig1_blixem.jpg     |  Bin 0 -> 687871 bytes
 src/doc/Publications/bmc_paper/fig2_dotter.jpg     |  Bin 0 -> 358328 bytes
 .../bmc_paper/fig3_belvu_conservation.png          |  Bin 0 -> 131393 bytes
 .../Publications/bmc_paper/fig4_belvu_residues.png |  Bin 0 -> 122186 bytes
 src/doc/Publications/bmc_paper/fig5_belvu_plot.png |  Bin 0 -> 24498 bytes
 src/doc/Publications/bmc_paper/fig6_belvu_tree.png |  Bin 0 -> 86198 bytes
 src/doc/Publications/bmc_paper/seqtools.bib        |  386 ++++
 src/doc/Publications/bmc_paper/seqtools.tex        |  436 +++++
 11 files changed, 2845 insertions(+)

2014-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Support old-style GFF from ZMap with only one CDS object
 src/seqtoolsUtils/blxmsp.c | 204 +++++++++++++++++++++++++++++++--------------
 1 file changed, 142 insertions(+), 62 deletions(-)

2014-06-09  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes
 src/doc/User_doc/release_notes.html | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

2014-06-09  Gemma Barson  <gb10@sanger.ac.uk>
 Dotter window layout now changes to maximise space
 src/dotterApp/dotter.c | 76 +++++++++++++++++++++++++++++++++-----------------
 1 file changed, 51 insertions(+), 25 deletions(-)

2014-06-09  Gemma Barson  <gb10@sanger.ac.uk>
 Improve layout of docked windows
 src/dotterApp/alignmenttool.c | 10 +++-------
 src/dotterApp/dotter.c        | 34 ++++++++++++++++++++++------------
 src/dotterApp/greyramptool.c  | 43 ++++++++++++++++++++++++++++---------------
 3 files changed, 53 insertions(+), 34 deletions(-)

2014-06-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fix off-by-one bug with dotter coords when length is even
 src/dotterApp/alignmenttool.c | 26 ++++++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

2014-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dock_windows' into develop
2014-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 More fixes for toggling windows. Also tidy frames
 src/dotterApp/alignmenttool.c | 48 +++++++++++++++++++++++++++++--------------
 src/dotterApp/greyramptool.c  | 32 ++++++++++++++++++++---------
 2 files changed, 55 insertions(+), 25 deletions(-)

2014-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Make sure menu is toggled when closing tools
 src/dotterApp/alignmenttool.c | 21 ++------------
 src/dotterApp/dotter.c        | 67 ++++++++++++++++++-------------------------
 src/dotterApp/dotter_.h       |  3 ++
 src/dotterApp/greyramptool.c  | 23 +++------------
 4 files changed, 38 insertions(+), 76 deletions(-)

2014-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to toggling dock/show/hide operations
 src/dotterApp/dotter.c        | 131 ++++++++++++++++++++++++++----------------
 src/seqtoolsUtils/utilities.c |  25 ++++++++
 src/seqtoolsUtils/utilities.h |   1 +
 3 files changed, 109 insertions(+), 48 deletions(-)

2014-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fix menu callbacks for alignment and greyramp tools
 src/dotterApp/alignmenttool.c | 55 ++++++++++++++++++++++++++++++-------------
 src/dotterApp/dotter_.h       |  4 ++--
 src/dotterApp/greyramptool.c  | 39 +++++++++++++++++++++++-------
 3 files changed, 70 insertions(+), 28 deletions(-)

2014-06-05  Gemma Barson  <gb10@sanger.ac.uk>
 Remove obsolete option to set alignment length
 src/dotterApp/alignmenttool.c | 92 -------------------------------------------
 1 file changed, 92 deletions(-)

2014-06-05  Gemma Barson  <gb10@sanger.ac.uk>
 Make sure menu toggle status keeps up to date with key press
 src/dotterApp/alignmenttool.c |  6 +++---
 src/dotterApp/dotter.c        | 25 ++++++++++++++++++-------
 src/dotterApp/greyramptool.c  |  6 +++---
 3 files changed, 24 insertions(+), 13 deletions(-)

2014-06-05  Gemma Barson  <gb10@sanger.ac.uk>
 Alignment tool now has dynamic width
 src/dotterApp/alignmenttool.c | 18 ++++++++++--------
 src/dotterApp/dotter.c        |  1 +
 src/dotterApp/dotter_.h       |  1 +
 3 files changed, 12 insertions(+), 8 deletions(-)

2014-06-05  Gemma Barson  <gb10@sanger.ac.uk>
 Keyboard shortcut for docking windows
 src/dotterApp/dotter.c | 12 ++++++++++++
 1 file changed, 12 insertions(+)

2014-06-05  Gemma Barson  <gb10@sanger.ac.uk>
 Docking of windows implemented
 src/dotterApp/alignmenttool.c |  10 +--
 src/dotterApp/dotter.c        | 142 ++++++++++++++++++++++++++++++++----------
 src/dotterApp/greyramptool.c  |  19 +++---
 3 files changed, 119 insertions(+), 52 deletions(-)

2014-06-05  Gemma Barson  <gb10@sanger.ac.uk>
 Reorganise tool widgets in preparation for being dockable
 src/dotterApp/alignmenttool.c | 44 ++++++++++++++++++++++++----------
 src/dotterApp/dotter.c        | 55 +++++++++++++++++++++++++++++--------------
 src/dotterApp/dotter_.h       |  4 ++--
 src/dotterApp/greyramptool.c  | 41 ++++++++++++++++++++++++--------
 4 files changed, 101 insertions(+), 43 deletions(-)

2014-06-02  Gemma Barson  <gb10@sanger.ac.uk>
 Small change to debug output
 src/blixemApp/blxwindow.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2014-05-29  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/gff' into develop
2014-05-29  Gemma Barson  <gb10@sanger.ac.uk>
 Tidying
 src/blixemApp/blixem_.h   | 2 +-
 src/blixemApp/blxFetch.c  | 2 +-
 src/blixemApp/blxview.c   | 6 +++---
 src/blixemApp/blxwindow.c | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

2014-05-29  Gemma Barson  <gb10@sanger.ac.uk>
 Tidying
 src/blixemApp/blixem_.h   |  6 +++---
 src/blixemApp/blxFetch.c  | 12 ++++++------
 src/blixemApp/blxview.c   |  2 +-
 src/blixemApp/blxwindow.c |  2 +-
 4 files changed, 11 insertions(+), 11 deletions(-)

2014-05-29  Gemma Barson  <gb10@sanger.ac.uk>
 Do range checking on imported file
 src/blixemApp/blixem_.h           |  6 +++---
 src/blixemApp/blxFetch.c          | 16 +++++++++-------
 src/blixemApp/blxmain.c           |  8 +-------
 src/blixemApp/blxview.c           | 17 +++++++++++++++--
 src/blixemApp/blxwindow.c         | 10 ++++++----
 src/seqtoolsUtils/blxGff3Parser.c | 40 +++++++++++++++++++++++++++++++--------
 src/seqtoolsUtils/blxGff3Parser.h |  3 ++-
 src/seqtoolsUtils/blxparser.c     | 10 +++++++++-
 8 files changed, 77 insertions(+), 33 deletions(-)

2014-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/drag_drop' into develop
2014-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Reset GFF ID lookup table when finished importing a file
 src/blixemApp/blixem_.h           | 11 ++---
 src/blixemApp/blxFetch.c          | 23 +++++++---
 src/blixemApp/blxmain.c           | 11 +++--
 src/blixemApp/blxview.c           | 12 +++---
 src/blixemApp/blxwindow.c         | 23 +++++++---
 src/dotterApp/dotterMain.c        |  7 ++-
 src/seqtoolsUtils/blxGff3Parser.c |  9 ++--
 src/seqtoolsUtils/blxGff3Parser.h |  3 +-
 src/seqtoolsUtils/blxmsp.c        | 89 +++++++++++++++++++++++++++------------
 src/seqtoolsUtils/blxmsp.h        |  6 +--
 src/seqtoolsUtils/blxparser.c     | 76 ++++++++++++++++++---------------
 src/seqtoolsUtils/blxparser.h     |  4 +-
 12 files changed, 174 insertions(+), 100 deletions(-)

2014-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Report how many features were imported by drag-and-drop
 src/blixemApp/blxview.c    |  9 +++------
 src/blixemApp/blxwindow.c  | 13 ++++++++++++-
 src/seqtoolsUtils/blxmsp.c |  2 +-
 3 files changed, 16 insertions(+), 8 deletions(-)

2014-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Support exons with multiple parents and mRNAs with multiple CDSs in the GFF
 src/seqtoolsUtils/blxGff3Parser.c |  19 ++-
 src/seqtoolsUtils/blxmsp.c        | 251 ++++++++++++++++++++++++++++++++++----
 src/seqtoolsUtils/blxmsp.h        |   3 +-
 3 files changed, 244 insertions(+), 29 deletions(-)

2014-05-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fix potential use of null source pointer
 src/seqtoolsUtils/blxGff3Parser.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-05-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with handling exons with multiple parents
 src/seqtoolsUtils/blxmsp.c | 37 +++++++++++++++++++++++++++++--------
 1 file changed, 29 insertions(+), 8 deletions(-)

2014-05-22  Gemma Barson  <gb10@sanger.ac.uk>
 GFF parser now supports multiple IDs in Parent tag
 src/seqtoolsUtils/blxmsp.c | 68 ++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 56 insertions(+), 12 deletions(-)

2014-05-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug constructing transcripts when exons and introns both given in file
 src/seqtoolsUtils/blxmsp.c | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

2014-05-22  Gemma Barson  <gb10@sanger.ac.uk>
 Add SNV to supported types
 src/seqtoolsUtils/blxGff3Parser.c | 1 +
 1 file changed, 1 insertion(+)

2014-05-22  Gemma Barson  <gb10@sanger.ac.uk>
 Recalculate grid range when importing features
 src/blixemApp/blxwindow.c | 4 ++++
 1 file changed, 4 insertions(+)

2014-05-22  Gemma Barson  <gb10@sanger.ac.uk>
 Tidying
 src/blixemApp/bigpicture.c | 61 ++++++++++++++++++++++++++++------------------
 src/blixemApp/blxview.c    |  9 +++++++
 2 files changed, 46 insertions(+), 24 deletions(-)

2014-05-21  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bugs parsing acedb-style gaps array
 src/blixemApp/blxwindow.c         |  2 +-
 src/seqtoolsUtils/blxGff3Parser.c | 27 +++++++++++++++++++++++++--
 src/seqtoolsUtils/blxparser.c     |  2 +-
 3 files changed, 27 insertions(+), 4 deletions(-)

2014-05-21  Gemma Barson  <gb10@sanger.ac.uk>
 Rename BLXSEQ_INVALID to BLXSEQ_NONE
 src/blixemApp/blxmain.c           | 10 +++++-----
 src/blixemApp/blxview.c           |  4 ++--
 src/blixemApp/blxwindow.c         |  2 +-
 src/dotterApp/dotterMain.c        | 12 ++++++------
 src/seqtoolsUtils/blxGff3Parser.c |  6 +++---
 src/seqtoolsUtils/blxparser.c     |  2 +-
 src/seqtoolsUtils/utilities.h     |  2 +-
 7 files changed, 19 insertions(+), 19 deletions(-)

2014-05-21  Gemma Barson  <gb10@sanger.ac.uk>
 Support legacy acedb-style gaps string in GFF for backwards compatibility
 src/seqtoolsUtils/blxGff3Parser.c | 24 ++++++++++++++++++++----
 src/seqtoolsUtils/blxparser.c     |  9 ++++-----
 src/seqtoolsUtils/blxparser.h     |  1 +
 3 files changed, 25 insertions(+), 9 deletions(-)

2014-05-21  Gemma Barson  <gb10@sanger.ac.uk>
 Filter matches from GFF by dna/protein mode
 src/blixemApp/blxmain.c           |  7 ++++++-
 src/dotterApp/dotterMain.c        |  2 +-
 src/seqtoolsUtils/blxGff3Parser.c | 14 +++++++++-----
 src/seqtoolsUtils/blxGff3Parser.h |  2 +-
 4 files changed, 17 insertions(+), 8 deletions(-)

2014-05-21  Gemma Barson  <gb10@sanger.ac.uk>
 Limit the number of warnings issue from the GFF parser
 src/seqtoolsUtils/blxGff3Parser.c | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

2014-05-16  Gemma Barson  <gb10@sanger.ac.uk>
 Debug
 src/dotterApp/dotter.c     | 4 ++--
 src/seqtoolsUtils/blxmsp.c | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

2014-05-16  Gemma Barson  <gb10@sanger.ac.uk>
 Tidying
 src/blixemApp/blxwindow.c  | 145 ++++++++++++++++++++++-----------------------
 src/blixemApp/detailview.c |  33 ++++++-----
 2 files changed, 87 insertions(+), 91 deletions(-)

2014-05-15  Gemma Barson  <gb10@sanger.ac.uk>
 Disable splice-site highlighting in dotter for protein seqs
 src/dotterApp/alignmenttool.c | 4 ++++
 1 file changed, 4 insertions(+)

2014-05-15  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes for 4.27
 src/doc/User_doc/release_notes.html | 10 ++++++++++
 1 file changed, 10 insertions(+)

2014-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Handle receiving of GFF file contents from drag-drop
 src/blixemApp/blixem_.h        |   6 +-
 src/blixemApp/blxFetch.c       |   6 +-
 src/blixemApp/blxmain.c        |   2 +-
 src/blixemApp/blxview.c        |  59 ++++++++-----
 src/blixemApp/blxwindow.c      |  56 +++++++++---
 src/blixemApp/blxwindow.h      |   3 +-
 src/blixemApp/detailviewtree.c |  32 ++++---
 src/seqtoolsUtils/blxparser.c  | 196 ++++++++++++++++++++++++++++-------------
 src/seqtoolsUtils/blxparser.h  |   3 +
 9 files changed, 245 insertions(+), 118 deletions(-)

2014-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Move drag-drop target type definition to utilities header
 src/seqtoolsUtils/utilities.h | 4 ++++
 1 file changed, 4 insertions(+)

2014-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Small improvements to debug output
 src/seqtoolsUtils/blxparser.c | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

2014-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Small improvements to debug output
 src/belvuApp/belvuTree.c          |  2 +-
 src/blixemApp/bigpicturegrid.c    |  2 +-
 src/blixemApp/blxwindow.c         | 13 ++++++++++++-
 src/seqtoolsUtils/blxGff3Parser.c | 14 +++++++-------
 4 files changed, 21 insertions(+), 10 deletions(-)

2014-05-07  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: Implement drop of drag-and-drop
 src/blixemApp/blxwindow.c      | 38 +++++++++++++++++++++++++++++++++++++-
 src/blixemApp/detailviewtree.c | 14 ++++++++++++++
 2 files changed, 51 insertions(+), 1 deletion(-)

2014-05-07  Gemma Barson  <gb10@sanger.ac.uk>
 Small improvement to layout of Find/Group dialog
 src/seqtoolsUtils/utilities.c | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

2014-05-07  Gemma Barson  <gb10@sanger.ac.uk>
 Hide filtered features from big picture as well as detail view
 src/blixemApp/bigpicturegrid.c | 42 +++++++++++++++++++++++++++++++++++++-----
 src/blixemApp/blxwindow.c      | 17 ++++++++++++++++-
 src/blixemApp/detailviewtree.c |  4 ++--
 src/blixemApp/exonview.c       | 36 +++++++++++++++++++++++++++++-------
 4 files changed, 84 insertions(+), 15 deletions(-)

2014-05-07  Gemma Barson  <gb10@sanger.ac.uk>
 Filter sequences and other features separately
 src/blixemApp/blixem_.h        |  3 ++-
 src/blixemApp/blxwindow.c      | 18 ++++++++++++------
 src/blixemApp/detailviewtree.c | 40 ++++++++++++++++++++++++++--------------
 3 files changed, 40 insertions(+), 21 deletions(-)

2014-05-01  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'production' into develop
2014-05-01  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'release/4.26' into develop
2014-05-01  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'release/4.26' into production
2014-04-25  Gemma Barson  <gb10@sanger.ac.uk>
 Change session_colour to session-colour in config
 src/seqtoolsUtils/blxmsp.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-04-25  Gemma Barson  <gb10@sanger.ac.uk>
 Change session_colour to session-colour in config
 src/seqtoolsUtils/blxmsp.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 Small update to running dotter in blixem manual
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf | Bin 1069254 -> 1058892 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex |   5 ++++-
 2 files changed, 4 insertions(+), 1 deletion(-)

2014-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dotter_splice_sites' into develop
2014-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 Documentation
 src/doc/User_doc/Dotter_manual/Dotter_manual.pdf | Bin 428996 -> 421271 bytes
 src/doc/User_doc/Dotter_manual/Dotter_manual.tex |   3 +++
 2 files changed, 3 insertions(+)

2014-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 Documentation and tooltips
 src/doc/User_doc/Dotter_manual/Dotter_manual.pdf   | Bin 437881 -> 428996 bytes
 src/doc/User_doc/Dotter_manual/Dotter_manual.tex   |   2 +-
 .../User_doc/Dotter_manual/img_dialog_settings.png | Bin 37779 -> 28910 bytes
 src/dotterApp/dotter.c                             |  15 ++++++++++-----
 4 files changed, 11 insertions(+), 6 deletions(-)

2014-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 Documentation and tooltips
 src/doc/User_doc/Dotter_manual/Dotter_manual.pdf | Bin 428718 -> 437881 bytes
 src/doc/User_doc/Dotter_manual/Dotter_manual.tex |  10 ++++++++--
 src/dotterApp/dotter.c                           |   3 +++
 3 files changed, 11 insertions(+), 2 deletions(-)

2014-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 Make splice-site highlighting configurable in the settings
 src/dotterApp/alignmenttool.c | 38 ++++++++++++++++++++++++++++++++++++++
 src/dotterApp/dotter.c        | 22 +++++++++++++++++++++-
 src/dotterApp/dotter_.h       |  2 ++
 3 files changed, 61 insertions(+), 1 deletion(-)

2014-04-17  Gemma Barson  <gb10@sanger.ac.uk>
 Splice sites are now highlighted in dotter's alignment tool
 src/dotterApp/alignmenttool.c | 100 +++++++++++++++++++++++++++++++++++++++++-
 src/dotterApp/dotter.c        |   2 +
 src/dotterApp/dotter_.h       |   2 +
 3 files changed, 102 insertions(+), 2 deletions(-)

2014-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fix crashes with showing hsps in dotter
 src/seqtoolsUtils/blxmsp.c | 41 ++++++++++++++++++++++-------------------
 1 file changed, 22 insertions(+), 19 deletions(-)

2014-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Add tooltips to dotter dialog
 src/blixemApp/blxdotter.c | 9 +++++++++
 1 file changed, 9 insertions(+)

2014-04-16  Gemma Barson  <gb10@sanger.ac.uk>
 Dotter auto coords now track big picture range
 src/blixemApp/bigpicture.c |  3 +++
 src/blixemApp/blxdotter.c  | 42 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+)

2014-04-02  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/session_colour' into develop
2014-04-02  Gemma Barson  <gb10@sanger.ac.uk>
 Make dotter's alignment/greyramp tool inherit the session colour
 src/dotterApp/dotter.c | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2014-04-02  Gemma Barson  <gb10@sanger.ac.uk>
 Send session_colour arg to dotter
 src/blixemApp/blixem_.h   | 1 +
 src/blixemApp/blxdotter.c | 3 +++
 src/blixemApp/blxwindow.c | 1 +
 3 files changed, 5 insertions(+)

2014-04-02  Gemma Barson  <gb10@sanger.ac.uk>
 Add session_colour arg to dotter
 src/dotterApp/dotter.c     | 22 ++++++++++++++--------
 src/dotterApp/dotter.h     |  2 ++
 src/dotterApp/dotterMain.c | 10 ++++++++++
 3 files changed, 26 insertions(+), 8 deletions(-)

2014-04-02  Gemma Barson  <gb10@sanger.ac.uk>
 Add session_colour config item
 src/blixemApp/blixem_.h       |  1 +
 src/blixemApp/blxFetch.c      |  3 +++
 src/blixemApp/blxwindow.c     |  7 ++++---
 src/blixemApp/detailview.c    | 20 ++++++++++++++------
 src/blixemApp/detailview.h    |  3 ++-
 src/seqtoolsUtils/blxmsp.h    |  1 +
 src/seqtoolsUtils/utilities.c | 14 ++++++++++++++
 src/seqtoolsUtils/utilities.h |  1 +
 8 files changed, 40 insertions(+), 10 deletions(-)

2014-03-18  Gemma Barson  <gb10@sanger.ac.uk>
 Update links to pdf manuals
 src/doc/User_doc/belvu_quick_start.html  | 2 +-
 src/doc/User_doc/blixem_quick_start.html | 2 +-
 src/doc/User_doc/dotter_quick_start.html | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

2014-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/docs' into develop
2014-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Remove old openoffice manuals
 src/Makefile.am                    |   4 ++--
 src/doc/User_doc/Belvu_manual.odt  | Bin 970146 -> 0 bytes
 src/doc/User_doc/Belvu_manual.pdf  | Bin 819868 -> 0 bytes
 src/doc/User_doc/Blixem_manual.odt | Bin 998860 -> 0 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 778696 -> 0 bytes
 src/doc/User_doc/Dotter_manual.odt | Bin 463997 -> 0 bytes
 src/doc/User_doc/Dotter_manual.pdf | Bin 342875 -> 0 bytes
 src/doc/User_doc/manuals.html      |  10 +++-------
 8 files changed, 5 insertions(+), 9 deletions(-)

2014-03-11  Gemma Barson  <gb10@sanger.ac.uk>
 Add screenshot of colinearity lines
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf   | Bin 984716 -> 1069254 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex   |  14 ++++++++++++--
 .../Blixem_manual/img_view_colinearity.png         | Bin 0 -> 118699 bytes
 3 files changed, 12 insertions(+), 2 deletions(-)

2014-03-11  Gemma Barson  <gb10@sanger.ac.uk>
 Update new settings dialog and colours in manual
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf | Bin 984856 -> 984716 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex | 577 ++++++++---------------
 2 files changed, 187 insertions(+), 390 deletions(-)

2014-03-11  Gemma Barson  <gb10@sanger.ac.uk>
 Remove references to authorised users
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf | Bin 985549 -> 984856 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex |  22 ++++------------------
 2 files changed, 4 insertions(+), 18 deletions(-)

2014-03-11  Gemma Barson  <gb10@sanger.ac.uk>
 Update blixem manual with sqlite config
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf | Bin 985476 -> 985549 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex | 266 +++++++++++++----------
 2 files changed, 148 insertions(+), 118 deletions(-)

2014-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 Add latex version of belvu manual
 src/doc/User_doc/Belvu_manual/Belvu_manual.pdf     | Bin 0 -> 893808 bytes
 src/doc/User_doc/Belvu_manual/Belvu_manual.tex     | 926 +++++++++++++++++++++
 .../Belvu_manual/img_dialog_find_sequences.png     | Bin 0 -> 21459 bytes
 .../Belvu_manual/img_dialog_plot_settings.png      | Bin 0 -> 20899 bytes
 .../User_doc/Belvu_manual/img_dialog_settings.png  | Bin 0 -> 42092 bytes
 src/doc/User_doc/Belvu_manual/img_menu_colour.png  | Bin 0 -> 24519 bytes
 .../Belvu_manual/img_menu_conservation_plot.png    | Bin 0 -> 8753 bytes
 src/doc/User_doc/Belvu_manual/img_menu_edit.png    | Bin 0 -> 44381 bytes
 src/doc/User_doc/Belvu_manual/img_menu_file.png    | Bin 0 -> 27662 bytes
 src/doc/User_doc/Belvu_manual/img_menu_help.png    | Bin 0 -> 4220 bytes
 .../User_doc/Belvu_manual/img_menu_settings.png    | Bin 0 -> 18945 bytes
 .../User_doc/Belvu_manual/img_menu_tear_offs.png   | Bin 0 -> 269813 bytes
 src/doc/User_doc/Belvu_manual/img_menu_tree.png    | Bin 0 -> 14906 bytes
 src/doc/User_doc/Belvu_manual/img_toolbar.png      | Bin 0 -> 10820 bytes
 .../img_window_alignment_by_conservation.png       | Bin 0 -> 152230 bytes
 .../img_window_alignment_by_residue.png            | Bin 0 -> 146877 bytes
 .../Belvu_manual/img_window_conservation_plot.png  | Bin 0 -> 26318 bytes
 .../User_doc/Belvu_manual/img_window_organisms.png | Bin 0 -> 17552 bytes
 src/doc/User_doc/Belvu_manual/img_window_tree.png  | Bin 0 -> 84334 bytes
 19 files changed, 926 insertions(+)

2014-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 Formatting
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf | Bin 982594 -> 985476 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex |  84 ++++++++++++++++-------
 src/doc/User_doc/Dotter_manual/Dotter_manual.pdf | Bin 425549 -> 428718 bytes
 src/doc/User_doc/Dotter_manual/Dotter_manual.tex |  26 +++++--
 4 files changed, 80 insertions(+), 30 deletions(-)

2014-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 Formatting
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf | Bin 995622 -> 982594 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex |  15 ++-
 src/doc/User_doc/Dotter_manual/Dotter_manual.pdf | Bin 421413 -> 425549 bytes
 src/doc/User_doc/Dotter_manual/Dotter_manual.tex | 112 ++++++++++++++++++++++-
 4 files changed, 120 insertions(+), 7 deletions(-)

2014-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 Add latex version of dotter manual
 src/doc/User_doc/Dotter_manual/Dotter_manual.pdf   | Bin 0 -> 421413 bytes
 src/doc/User_doc/Dotter_manual/Dotter_manual.tex   | 890 +++++++++++++++++++++
 .../User_doc/Dotter_manual/img_dialog_settings.png | Bin 0 -> 37779 bytes
 .../Dotter_manual/img_menu_alignment_tool.png      | Bin 0 -> 7513 bytes
 src/doc/User_doc/Dotter_manual/img_menu_edit.png   | Bin 0 -> 6088 bytes
 src/doc/User_doc/Dotter_manual/img_menu_file.png   | Bin 0 -> 19028 bytes
 src/doc/User_doc/Dotter_manual/img_menu_help.png   | Bin 0 -> 4220 bytes
 .../User_doc/Dotter_manual/img_menu_tear_off.png   | Bin 0 -> 55318 bytes
 src/doc/User_doc/Dotter_manual/img_menu_view.png   | Bin 0 -> 24076 bytes
 .../Dotter_manual/img_window_dotter_self.png       | Bin 0 -> 77462 bytes
 .../User_doc/Dotter_manual/img_window_greyramp.png | Bin 0 -> 11103 bytes
 src/doc/User_doc/Dotter_manual/img_window_main.png | Bin 0 -> 52361 bytes
 .../Dotter_manual/img_window_nucleotide.png        | Bin 0 -> 32253 bytes
 .../User_doc/Dotter_manual/img_window_protein.png  | Bin 0 -> 39627 bytes
 14 files changed, 890 insertions(+)

2014-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 Formatting
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf | Bin 976653 -> 995622 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex |  27 +++++++++++------------
 2 files changed, 13 insertions(+), 14 deletions(-)

2014-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 Ignore latex generated files
 .gitignore | 5 +++++
 1 file changed, 5 insertions(+)

2014-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 Add latex version of blixem manual
 src/doc/User_doc/Blixem_manual/Blixem_manual.pdf   |  Bin 0 -> 976653 bytes
 src/doc/User_doc/Blixem_manual/Blixem_manual.tex   | 2421 ++++++++++++++++++++
 .../User_doc/Blixem_manual/img_button_about.png    |  Bin 0 -> 1351 bytes
 .../Blixem_manual/img_button_back_base.png         |  Bin 0 -> 925 bytes
 .../Blixem_manual/img_button_back_page.png         |  Bin 0 -> 936 bytes
 src/doc/User_doc/Blixem_manual/img_button_find.png |  Bin 0 -> 1368 bytes
 .../Blixem_manual/img_button_first_match.png       |  Bin 0 -> 1265 bytes
 .../Blixem_manual/img_button_forward_base.png      |  Bin 0 -> 907 bytes
 .../Blixem_manual/img_button_forward_page.png      |  Bin 0 -> 931 bytes
 .../User_doc/Blixem_manual/img_button_go_to.png    |  Bin 0 -> 1403 bytes
 src/doc/User_doc/Blixem_manual/img_button_help.png |  Bin 0 -> 1590 bytes
 .../Blixem_manual/img_button_last_match.png        |  Bin 0 -> 1279 bytes
 .../Blixem_manual/img_button_next_match.png        |  Bin 0 -> 1175 bytes
 .../Blixem_manual/img_button_prev_match.png        |  Bin 0 -> 1183 bytes
 .../User_doc/Blixem_manual/img_button_settings.png |  Bin 0 -> 1541 bytes
 src/doc/User_doc/Blixem_manual/img_button_sort.png |  Bin 0 -> 1007 bytes
 .../Blixem_manual/img_button_toggle_strand.png     |  Bin 0 -> 1527 bytes
 .../User_doc/Blixem_manual/img_button_zoom_in.png  |  Bin 0 -> 1385 bytes
 .../Blixem_manual/img_button_zoom_in_bp.png        |  Bin 0 -> 1199 bytes
 .../User_doc/Blixem_manual/img_button_zoom_out.png |  Bin 0 -> 1371 bytes
 .../Blixem_manual/img_button_zoom_out_bp.png       |  Bin 0 -> 1288 bytes
 .../Blixem_manual/img_button_zoom_whole_bp.png     |  Bin 0 -> 1308 bytes
 .../User_doc/Blixem_manual/img_dialog_dotter.png   |  Bin 0 -> 30483 bytes
 src/doc/User_doc/Blixem_manual/img_dialog_find.png |  Bin 0 -> 25336 bytes
 .../User_doc/Blixem_manual/img_dialog_groups.png   |  Bin 0 -> 27662 bytes
 .../Blixem_manual/img_dialog_groups_edit.png       |  Bin 0 -> 32867 bytes
 src/doc/User_doc/Blixem_manual/img_dialog_sort.png |  Bin 0 -> 23923 bytes
 src/doc/User_doc/Blixem_manual/img_dialog_view.png |  Bin 0 -> 78987 bytes
 .../Blixem_manual/img_menu_right_click.png         |  Bin 0 -> 15910 bytes
 src/doc/User_doc/Blixem_manual/img_toolbar.png     |  Bin 0 -> 11617 bytes
 .../img_view_alignment_colour_key.png              |  Bin 0 -> 34900 bytes
 .../Blixem_manual/img_view_alignment_details.png   |  Bin 0 -> 53288 bytes
 .../img_view_alignment_details_nucleotide.png      |  Bin 0 -> 70983 bytes
 .../img_view_alignment_details_protein.png         |  Bin 0 -> 86757 bytes
 .../img_view_alignment_list_exons.png              |  Bin 0 -> 27697 bytes
 .../Blixem_manual/img_view_big_picture.png         |  Bin 0 -> 14903 bytes
 .../User_doc/Blixem_manual/img_view_coverage.png   |  Bin 0 -> 6224 bytes
 .../Blixem_manual/img_view_feedback_area.png       |  Bin 0 -> 3082 bytes
 .../Blixem_manual/img_view_feedback_box.png        |  Bin 0 -> 18914 bytes
 .../Blixem_manual/img_view_reading_frame.png       |  Bin 0 -> 97169 bytes
 .../Blixem_manual/img_view_selected_codon.png      |  Bin 0 -> 8573 bytes
 .../Blixem_manual/img_view_sort_by_group.png       |  Bin 0 -> 28427 bytes
 .../Blixem_manual/img_view_transcripts.png         |  Bin 0 -> 19353 bytes
 .../User_doc/Blixem_manual/img_view_variations.png |  Bin 0 -> 14011 bytes
 .../Blixem_manual/img_window_nucleotide_mode.png   |  Bin 0 -> 91951 bytes
 .../Blixem_manual/img_window_protein_mode.png      |  Bin 0 -> 96739 bytes
 46 files changed, 2421 insertions(+)

2014-03-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fix potential crash in new polyA tail code
 src/blixemApp/detailview.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2014-03-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug where Mets and Stops weren't being highlighted
 src/blixemApp/detailview.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Add autogen.sh and make runconfig args more sensible
 src/autogen.sh   | 14 ++++++++++++++
 src/runconfig.sh |  5 +++--
 2 files changed, 17 insertions(+), 2 deletions(-)

2014-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Call dotter on same screen as blixem
 src/blixemApp/blxdotter.c | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

2014-03-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix error with GTK args not being recognised
 src/belvuApp/belvuMain.c   | 2 ++
 src/blixemApp/blxmain.c    | 2 ++
 src/dotterApp/dotterMain.c | 2 ++
 3 files changed, 6 insertions(+)

2014-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Grey out mouse-over tickboxes if not applicable
 src/blixemApp/blxview.c    | 42 +++++++++++++++++++++---------------------
 src/blixemApp/blxwindow.c  | 33 ++++++++++++++++++++++-----------
 src/dotterApp/dotter.c     |  2 +-
 src/seqtoolsUtils/blxmsp.c |  6 ++++++
 src/seqtoolsUtils/blxmsp.h |  3 ++-
 5 files changed, 52 insertions(+), 34 deletions(-)

2014-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Make mouse-over details configurable
 src/blixemApp/blixem_.h    |  5 +++-
 src/blixemApp/blxview.c    | 54 ++++++++++++++++++++++++++++++----
 src/blixemApp/blxwindow.c  | 73 +++++++++++++++++++++++++++++++++++++---------
 src/blixemApp/detailview.c | 19 ++++++++++++
 src/blixemApp/detailview.h |  1 +
 5 files changed, 132 insertions(+), 20 deletions(-)

2014-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bugs to do with multiple fasta seqs in GFF file
 src/seqtoolsUtils/blxGff3Parser.c | 59 ++++++++++++++++++++++++++-------------
 src/seqtoolsUtils/blxGff3Parser.h |  1 +
 src/seqtoolsUtils/blxparser.c     | 14 ++++++++++
 3 files changed, 54 insertions(+), 20 deletions(-)

2014-03-04  Gemma Barson  <gb10@sanger.ac.uk>
 Remove garbage file that was added by mistake
 src/dotterApp/dotterWindow | 1827 --------------------------------------------
 1 file changed, 1827 deletions(-)

2014-03-04  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/polya' into develop
2014-03-04  Gemma Barson  <gb10@sanger.ac.uk>
 Fix polyA boundary and coord direction when display reversed
 src/blixemApp/detailview.c | 38 +++++++++++++++++++++++++++++---------
 1 file changed, 29 insertions(+), 9 deletions(-)

2014-03-03  Gemma Barson  <gb10@sanger.ac.uk>
 Display info about moused-over polyA signals and sites
 src/blixemApp/detailview.c | 164 +++++++++++++++++++++++++++++++++++++++++----
 src/blixemApp/detailview.h |  10 ---
 2 files changed, 152 insertions(+), 22 deletions(-)

2014-02-28  Gemma Barson  <gb10@sanger.ac.uk>
 Highlight polyA sites in the reference sequence
 src/blixemApp/blixem_.h    |  3 ++
 src/blixemApp/blxwindow.c  |  9 +++--
 src/blixemApp/detailview.c | 87 +++++++++++++++++++++++++++++++++++++---------
 3 files changed, 80 insertions(+), 19 deletions(-)

2014-02-28  Gemma Barson  <gb10@sanger.ac.uk>
 Check entire unaligned sequence for polyA tail instead of limited number of bases
 src/seqtoolsUtils/blxmsp.c | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

2014-02-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with finding polyA signals when revcompd
 src/blixemApp/detailview.c | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

2014-02-28  Gemma Barson  <gb10@sanger.ac.uk>
 Scan for polyA signals in ref seq
 src/blixemApp/detailview.c | 49 ++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 43 insertions(+), 6 deletions(-)

2014-02-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug with showing polyA signals for selected sequences
 src/blixemApp/detailview.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2014-02-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix some bugs caused by previous tidying
 src/blixemApp/detailview.c     |  7 ++++++-
 src/blixemApp/detailviewtree.c | 11 +++++------
 2 files changed, 11 insertions(+), 7 deletions(-)

2014-02-28  Gemma Barson  <gb10@sanger.ac.uk>
 Tidying
 src/seqtoolsUtils/blxmsp.c | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

2014-02-27  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: check matches for polyA tails
 src/blixemApp/blxview.c              |  2 +-
 src/blixemApp/detailview.c           |  2 +-
 src/blixemApp/sequencecellrenderer.c |  2 +-
 src/seqtoolsUtils/blxmsp.c           | 82 +++++++++++++++++++++++++++---------
 src/seqtoolsUtils/blxmsp.h           |  4 +-
 5 files changed, 68 insertions(+), 24 deletions(-)

2012-11-01  Gemma Barson  <gb10@sanger.ac.uk>
 WIP
 src/blixemApp/detailview.c     | 78 +++++++++++++++++++++---------------------
 src/blixemApp/detailview.h     |  6 ++++
 src/blixemApp/detailviewtree.c |  2 +-
 3 files changed, 46 insertions(+), 40 deletions(-)

2012-10-24  Gemma Barson  <gb10@sanger.ac.uk>
 Tidy reference sequence highlighting code
 src/blixemApp/detailview.c     | 72 +++++++++++++++++++++---------------------
 src/blixemApp/detailview.h     | 33 +++++++++++--------
 src/blixemApp/detailviewtree.c | 10 +++---
 3 files changed, 62 insertions(+), 53 deletions(-)

2014-02-27  Gemma Barson  <gb10@sanger.ac.uk>
 Scrollwheel now scrolls big picture separately to detail view (RT206070)
 src/blixemApp/bigpicture.c     | 97 ++++++++++++++++++++++++++++++++++++------
 src/blixemApp/bigpicture.h     |  2 +
 src/blixemApp/bigpicturegrid.c | 11 +----
 src/blixemApp/coverageview.c   | 10 +----
 src/blixemApp/detailview.c     | 19 ++++++++-
 src/blixemApp/detailview.h     |  2 +
 src/blixemApp/exonview.c       |  6 +--
 7 files changed, 112 insertions(+), 35 deletions(-)

2014-02-27  Gemma Barson  <gb10@sanger.ac.uk>
 Improve warnings if fetch returns invalid data
 src/blixemApp/blxFetch.c | 43 +++++++++++++++++++++++++++++++++++++------
 1 file changed, 37 insertions(+), 6 deletions(-)

2014-02-26  Gemma Barson  <gb10@sanger.ac.uk>
 Remove unused x options so only 2 file args possible (RT288114)
 src/blixemApp/blxdotter.c  | 15 +++++--------
 src/dotterApp/dotter.h     |  1 -
 src/dotterApp/dotterMain.c | 56 +++++-----------------------------------------
 3 files changed, 12 insertions(+), 60 deletions(-)

2014-02-26  Gemma Barson  <gb10@sanger.ac.uk>
 Go-to-position dialog now has option to specify toplevel coords
 src/blixemApp/detailview.c | 34 ++++++++++++++++++++++++++++------
 1 file changed, 28 insertions(+), 6 deletions(-)

2014-02-25  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes
 src/doc/User_doc/release_notes.html | 8 ++++++++
 1 file changed, 8 insertions(+)

2014-02-25  Gemma Barson  <gb10@sanger.ac.uk>
 Update gitignore
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

2014-02-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with traffic light lines in protein mode
 src/blixemApp/detailviewtree.c       |  2 +-
 src/blixemApp/sequencecellrenderer.c | 43 +++++++++++++++++++++++++-----------
 2 files changed, 31 insertions(+), 14 deletions(-)

2014-02-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with unaligned seq being shown for all seqs
 src/blixemApp/blxview.c              | 15 ++++++++++++---
 src/blixemApp/sequencecellrenderer.c |  4 ----
 2 files changed, 12 insertions(+), 7 deletions(-)

2014-02-24  Gemma Barson  <gb10@sanger.ac.uk>
 Update repo gitignore
 .gitignore | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2014-02-24  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/traffic_light' into develop
2014-02-20  Gemma Barson  <gb10@sanger.ac.uk>
 Show colinearity lines in normal (unsquashed) mode
 src/blixemApp/sequencecellrenderer.c | 68 +++++++++++++++++++++++++++++++++---
 1 file changed, 63 insertions(+), 5 deletions(-)

2014-02-20  Gemma Barson  <gb10@sanger.ac.uk>
 Make show-colinearity optional
 src/blixemApp/bigpicturegrid.c       | 10 +++--
 src/blixemApp/blixem_.h              |  6 ++-
 src/blixemApp/blxwindow.c            | 15 +++++--
 src/blixemApp/sequencecellrenderer.c | 83 +++++++++++++++++++-----------------
 4 files changed, 69 insertions(+), 45 deletions(-)

2014-02-20  Gemma Barson  <gb10@sanger.ac.uk>
 Show colinearity lines in squashed view
 src/blixemApp/sequencecellrenderer.c | 61 ++++++++++++++++++++++++++++++++++--
 1 file changed, 59 insertions(+), 2 deletions(-)

2014-02-20  Gemma Barson  <gb10@sanger.ac.uk>
 Commenting and small fix
 src/blixemApp/sequencecellrenderer.c | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

2014-02-20  Gemma Barson  <gb10@sanger.ac.uk>
 Tidying
 src/blixemApp/sequencecellrenderer.c | 277 ++++++++++++++++++-----------------
 1 file changed, 140 insertions(+), 137 deletions(-)

2014-02-20  Gemma Barson  <gb10@sanger.ac.uk>
 Add traffic-light lines to top view
 src/blixemApp/bigpicturegrid.c | 124 +++++++++++++++++++++++++++++++++--------
 src/blixemApp/blixem_.h        |   3 +
 src/blixemApp/blxwindow.c      |   5 ++
 src/seqtoolsUtils/blxmsp.c     |  43 +++++++++++---
 src/seqtoolsUtils/blxmsp.h     |   2 +
 src/seqtoolsUtils/utilities.h  |  12 +++-
 6 files changed, 157 insertions(+), 32 deletions(-)

2014-02-19  Gemma Barson  <gb10@sanger.ac.uk>
 Add windows installation documentation to dist
 src/Makefile.am | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-02-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fix problem with abstract type flag
 src/blixemApp/sequencecellrenderer.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-02-07  Jeremy Henty  <jh13@sanger.ac.uk>
 blxFetchDb.c: fix comment typo.
 src/blixemApp/blxFetchDb.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-01-31  Jeremy Henty  <jh13@sanger.ac.uk>
 blxmain.c: main(): reword a misleading comment.
 src/blixemApp/blxmain.c | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

2014-01-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with sorting in belvu
 src/belvuApp/belvuWindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2014-01-21  Gemma Barson  <gb10@sanger.ac.uk>
 Fix problem with abstract type flag
 src/blixemApp/sequencecellrenderer.c | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

2014-01-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fix g++ compiler warnings
 src/belvuApp/belvu.c                   | 136 +++++++++++-----------
 src/belvuApp/belvuAlignment.c          |  18 +--
 src/belvuApp/belvuConsPlot.c           |   6 +-
 src/belvuApp/belvuMain.c               |  16 +--
 src/belvuApp/belvuTree.c               |  94 ++++++++--------
 src/belvuApp/belvuWindow.c             |  48 ++++----
 src/belvuApp/belvu_.h                  |  12 +-
 src/blixemApp/bigpicture.c             |  38 +++----
 src/blixemApp/bigpicture.h             |   4 +-
 src/blixemApp/bigpicturegrid.c         |  12 +-
 src/blixemApp/blixem_.h                |  28 ++---
 src/blixemApp/blxFetch.c               |  44 ++++----
 src/blixemApp/blxFetchDb.c             |   1 +
 src/blixemApp/blxdotter.c              |  32 +++---
 src/blixemApp/blxmain.c                |   8 +-
 src/blixemApp/blxview.c                | 142 ++++++++---------------
 src/blixemApp/blxwindow.c              |  70 ++++++------
 src/blixemApp/blxwindow.h              |   2 +-
 src/blixemApp/coverageview.c           |   4 +-
 src/blixemApp/detailview.c             | 112 +++++++++----------
 src/blixemApp/detailview.h             |   8 +-
 src/blixemApp/detailviewtree.c         |  46 ++++----
 src/blixemApp/detailviewtree.h         |   2 +-
 src/blixemApp/exonview.c               |  28 ++---
 src/blixemApp/sequencecellrenderer.c   |  53 ++++-----
 src/dotterApp/alignmenttool.c          |  12 +-
 src/dotterApp/dotplot.c                |  38 +++----
 src/dotterApp/dotter.c                 |  59 ++++++----
 src/dotterApp/dotterKarlin.c           |  14 +--
 src/dotterApp/dotterMain.c             |  36 +++---
 src/dotterApp/dotter_.h                |  21 ++--
 src/dotterApp/greyramptool.c           |   6 +-
 src/dotterApp/seqtoolsExonView.c       |  14 +--
 src/dotterApp/seqtoolsExonView.h       |   2 +-
 src/seqtoolsUtils/blxGff3Parser.c      |  34 +++---
 src/seqtoolsUtils/blxGff3Parser.h      |   2 +-
 src/seqtoolsUtils/blxmsp.c             | 198 +++++++++++++++++++++------------
 src/seqtoolsUtils/blxmsp.h             | 115 ++++++++++---------
 src/seqtoolsUtils/blxparser.c          |  22 ++--
 src/seqtoolsUtils/iupac.h              |   4 +-
 src/seqtoolsUtils/seqtoolsWebBrowser.c |  12 +-
 src/seqtoolsUtils/translate.c          |   2 +-
 src/seqtoolsUtils/utilities.c          | 165 +++++++++++++--------------
 src/seqtoolsUtils/utilities.h          |  74 ++++++------
 44 files changed, 916 insertions(+), 878 deletions(-)

2014-01-29  Steve Miller  <sm23@sanger.ac.uk>
 Merge branch 'release/4.25' into production
2014-01-16  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes
 src/doc/User_doc/release_notes.html | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

2014-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix potential crash in shutting down dotter
 src/seqtoolsUtils/blxmsp.c | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

2014-01-09  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/sqlite' into develop
2014-01-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fix backwards compatibility issue with optional-fetch methods
 src/blixemApp/blxFetch.c | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

2014-01-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fix memory corruption due to bad column info struct
 src/blixemApp/blxwindow.c  |  6 +++---
 src/blixemApp/detailview.h | 22 +---------------------
 2 files changed, 4 insertions(+), 24 deletions(-)

2014-01-03  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/sqlite
2014-01-02  Gemma Barson  <gb10@sanger.ac.uk>
 Docs: instructions to install with cygwin
 src/INSTALL         | 12 +++++-----
 src/INSTALL.windows | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 70 insertions(+), 6 deletions(-)

2013-12-23  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'release/4.24' into production
2013-11-27  Gemma Barson  <gb10@sanger.ac.uk>
 Portability improvements
 src/configure.ac              | 3 +++
 src/seqtoolsUtils/utilities.c | 8 ++++++++
 2 files changed, 11 insertions(+)

2013-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Update release notes
 src/doc/User_doc/release_notes.html | 45 +++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

2013-11-11  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2013-11-11  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.23' into production
2013-11-11  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/sqlite
2013-11-07  Jeremy Henty  <jh13@sanger.ac.uk>
 Typo fix: feaature -> feature.
 src/blixemApp/blxwindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2013-10-30  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug in keyword substitutions
 src/blixemApp/blxFetch.c | 74 +++++++++++++++++++++++++++++++++---------------
 1 file changed, 51 insertions(+), 23 deletions(-)

2013-10-30  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug in keyword substitutions
 src/blixemApp/blxFetch.c | 74 +++++++++++++++++++++++++++++++++---------------
 1 file changed, 51 insertions(+), 23 deletions(-)

2013-10-30  Gemma Barson  <gb10@sanger.ac.uk>
 Fix merge error
 src/blixemApp/blixem_.h | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2013-10-30  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/sqlite
2013-10-30  Gemma Barson  <gb10@sanger.ac.uk>
 Allow key names in substitution variables
 src/blixemApp/blixem_.h   |  15 +++-
 src/blixemApp/blxFetch.c  | 210 ++++++++++++++++++++++++++++++----------------
 src/blixemApp/blxwindow.c |  11 +--
 3 files changed, 155 insertions(+), 81 deletions(-)

2013-10-24  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/sqlite
2013-10-24  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.23' into develop
2013-10-24  Gemma Barson  <gb10@sanger.ac.uk>
 For now, use Gap string if given instead of cigar_bam
 src/seqtoolsUtils/blxGff3Parser.c | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

2013-10-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fixes for reading the cigar_bam gap string
 src/seqtoolsUtils/blxGff3Parser.c | 48 +++++++++++++++++++++++----------------
 1 file changed, 29 insertions(+), 19 deletions(-)

2013-10-24  Gemma Barson  <gb10@sanger.ac.uk>
 For now, use Gap string if given instead of cigar_bam
 src/seqtoolsUtils/blxGff3Parser.c | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

2013-10-22  Gemma Barson  <gb10@sanger.ac.uk>
 Allow dataType to be specified in source stanza
 src/seqtoolsUtils/blxGff3Parser.c | 50 ++++++++++++++++++++++++++++++++++-----
 1 file changed, 44 insertions(+), 6 deletions(-)

2013-10-21  Gemma Barson  <gb10@sanger.ac.uk>
 Fix merge errors
 src/blixemApp/blixem_.h        |   5 +-
 src/blixemApp/blxFetch.c       |   2 +-
 src/blixemApp/blxwindow.c      | 138 +++++++++++++-----------
 src/blixemApp/blxwindow.h      |   2 +
 src/blixemApp/detailviewtree.c |   1 +
 src/dotterApp/dotterMain.c     |   2 +-
 src/seqtoolsUtils/blxmsp.c     | 234 +----------------------------------------
 src/seqtoolsUtils/blxmsp.h     |   3 +-
 8 files changed, 90 insertions(+), 297 deletions(-)

2013-10-16  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/sqlite
2013-10-07  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'release/4.22' into production
2013-08-28  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2013-08-28  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.21' into production
2013-08-20  Gemma Barson  <gb10@sanger.ac.uk>
 Handling of cigar_bam tag in GFF3
 src/seqtoolsUtils/blxGff3Parser.c | 381 ++++++++++++++++++++++++++++----------
 1 file changed, 288 insertions(+), 93 deletions(-)

2013-08-05  Gemma Barson  <gb10@sanger.ac.uk>
 Make sure dotter doesn't try to use X if it's not required
 src/dotterApp/dotter.c     | 31 ++++++++++++++++++++-----------
 src/dotterApp/dotterMain.c | 10 ++++++----
 2 files changed, 26 insertions(+), 15 deletions(-)

2013-06-25  Gemma Barson  <gb10@sanger.ac.uk>
 Add a Clear button to the Find dialog in Blixem
 src/belvuApp/belvuWindow.c    |  4 +--
 src/blixemApp/blxwindow.c     | 82 +++++++++++++++++++++++++++++++++++--------
 src/seqtoolsUtils/utilities.c |  9 +++--
 src/seqtoolsUtils/utilities.h |  9 +++--
 4 files changed, 82 insertions(+), 22 deletions(-)

2013-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/config' into develop
2013-06-05  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented squash-linked-features config option
 src/blixemApp/detailview.c     |  3 ++-
 src/blixemApp/detailviewtree.c | 61 ++++++++++++++++++++++++++++++++----------
 src/blixemApp/detailviewtree.h |  2 +-
 3 files changed, 50 insertions(+), 16 deletions(-)

2013-06-05  Gemma Barson  <gb10@sanger.ac.uk>
 Move hard-coded short-read display code to config
 src/blixemApp/blixem_.h              |   6 +-
 src/blixemApp/blxFetch.c             |  14 +-
 src/blixemApp/blxview.c              |   2 +-
 src/blixemApp/blxwindow.c            |   5 +-
 src/blixemApp/detailview.c           |   5 +-
 src/blixemApp/detailview.h           |   4 +-
 src/blixemApp/detailviewtree.c       |  65 ++++++----
 src/blixemApp/sequencecellrenderer.c |   7 +-
 src/dotterApp/dotterMain.c           |   2 +-
 src/seqtoolsUtils/blxGff3Parser.c    |  87 +++++--------
 src/seqtoolsUtils/blxmsp.c           | 244 ++++++++++++++++++++++++++---------
 src/seqtoolsUtils/blxmsp.h           |  56 +++++---
 src/seqtoolsUtils/blxparser.c        |  12 +-
 13 files changed, 325 insertions(+), 184 deletions(-)

2013-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Add %g substitution argument to allow config of GFF version (RT332510)
 src/blixemApp/blxFetch.c      | 4 ++++
 src/seqtoolsUtils/utilities.h | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

2013-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Bounds limit dotter range when using big-picture range
 src/blixemApp/blxdotter.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

2013-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Add sequence-type arguments to dotter so it does not have to guess (RT330489)
 src/blixemApp/blixem_.h    |  2 +-
 src/blixemApp/blxdotter.c  |  8 +++++++
 src/dotterApp/dotterMain.c | 60 +++++++++++++++++++++++++++++++++++++---------
 3 files changed, 58 insertions(+), 12 deletions(-)

2013-05-08  Gemma Barson  <gb10@sanger.ac.uk>
 New colour scheme (RT329278)
 src/blixemApp/blxwindow.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2013-05-08  Gemma Barson  <gb10@sanger.ac.uk>
 New colour scheme (RT329278)
 src/blixemApp/blxwindow.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

2013-05-08  Gemma Barson  <gb10@sanger.ac.uk>
 Incorrect colour was being used for background
 src/blixemApp/sequencecellrenderer.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2013-05-07  Gemma Barson  <gb10@sanger.ac.uk>
 Improve toolbar layout for small screens
 src/blixemApp/detailview.c | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

2013-05-07  Gemma Barson  <gb10@sanger.ac.uk>
 Improve settings dialog mnemonics
 src/blixemApp/blxwindow.c | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

2013-05-07  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem support for small screens
 src/blixemApp/blxwindow.c  | 222 ++++++++++++++++++++++++++-------------------
 src/blixemApp/detailview.c |   2 +-
 2 files changed, 130 insertions(+), 94 deletions(-)

2013-04-19  Gemma Barson  <gb10@sanger.ac.uk>
 Enable splice site highlighting by default
 src/blixemApp/blxwindow.c | 1 +
 1 file changed, 1 insertion(+)

2013-04-09  Ed Griffiths  <edgrif@sanger.ac.uk>
 Merge branch 'release/4.20' into production
2013-03-05  Gemma Barson  <gb10@sanger.ac.uk>
 Fix problem with addressing null error
 src/blixemApp/blxFetch.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2013-03-05  Gemma Barson  <gb10@sanger.ac.uk>
 Protect against freeing null GStrings
 src/blixemApp/blxFetch.c | 27 +++++++++++++++++++++------
 1 file changed, 21 insertions(+), 6 deletions(-)

2013-02-01  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.19' into production
2013-02-01  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

2012-11-30  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2012-11-30  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.18' into production
2012-11-22  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem usage now printed to stdout, with successful exit code
 src/belvuApp/belvuMain.c   | 32 +++++++++++++--------
 src/blixemApp/blxmain.c    | 36 ++++++++++++++----------
 src/dotterApp/dotterMain.c | 69 +++++++++++++++++++++++++++-------------------
 3 files changed, 82 insertions(+), 55 deletions(-)

2012-11-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a regression where user-entered depth per cell was being ignored
 src/blixemApp/coverageview.c | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

2012-11-15  Gemma Barson  <gb10@sanger.ac.uk>
 Coverage view depth labels are now abbreviated e.g. 1000 => 1k
 src/blixemApp/bigpicture.c     | 79 +++++++++++++++++++++++++++++++++++-------
 src/blixemApp/bigpicture.h     |  2 +-
 src/blixemApp/bigpicturegrid.c |  2 +-
 src/blixemApp/coverageview.c   |  2 +-
 4 files changed, 70 insertions(+), 15 deletions(-)

2012-11-15  Gemma Barson  <gb10@sanger.ac.uk>
 Improve coverage view scale
 src/blixemApp/bigpicture.c    | 35 --------------------
 src/blixemApp/coverageview.c  | 66 ++++++++++++++++++++++++-------------
 src/seqtoolsUtils/utilities.c | 75 +++++++++++++++++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |  2 ++
 4 files changed, 120 insertions(+), 58 deletions(-)

2012-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Change abbrev-title default to false for blixem and dotter
 src/blixemApp/blxmain.c    | 2 +-
 src/dotterApp/dotterMain.c | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

2012-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Add option to abbreviate belvu window titles
 src/belvuApp/belvu.c         |  42 +++++++++++++
 src/belvuApp/belvuConsPlot.c |  13 +++-
 src/belvuApp/belvuMain.c     |  11 +++-
 src/belvuApp/belvuTree.c     |  11 +++-
 src/belvuApp/belvuWindow.c   | 144 ++++++++++++++++++++++++++-----------------
 src/belvuApp/belvu_.h        |  11 ++++
 6 files changed, 166 insertions(+), 66 deletions(-)

2012-11-14  Gemma Barson  <gb10@sanger.ac.uk>
 Add option to abbreviate window title prefixes in blixem and dotter
 src/blixemApp/blixem_.h       |  12 +++++
 src/blixemApp/blxFetch.c      |   9 ++--
 src/blixemApp/blxdotter.c     |  16 +++++--
 src/blixemApp/blxmain.c       |  19 +++++++-
 src/blixemApp/blxview.c       |  60 +++++++++++++++++++++--
 src/blixemApp/blxwindow.c     | 108 +++++++++++++++++++++++-------------------
 src/blixemApp/detailview.c    |   8 +++-
 src/dotterApp/alignmenttool.c |  15 ++++--
 src/dotterApp/dotter.c        |  89 +++++++++++++++++++---------------
 src/dotterApp/dotter.h        |   1 +
 src/dotterApp/dotterMain.c    |  14 +++++-
 src/dotterApp/dotter_.h       |  14 +++++-
 src/dotterApp/greyramptool.c  |   7 ++-
 13 files changed, 259 insertions(+), 113 deletions(-)

2012-11-05  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.17' into production
2012-10-17  Gemma Barson  <gb10@sanger.ac.uk>
 Look for styles when using the load-features-file option
 src/blixemApp/blixem_.h   |   2 +
 src/blixemApp/blxmain.c   | 343 ----------------------------------------------
 src/blixemApp/blxview.c   | 343 ++++++++++++++++++++++++++++++++++++++++++++++
 src/blixemApp/blxwindow.c |   3 +-
 4 files changed, 347 insertions(+), 344 deletions(-)

2012-10-17  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/loadfile' into develop
2012-10-16  Gemma Barson  <gb10@sanger.ac.uk>
 Updated incorrect tooltip shortcut text
 src/blixemApp/blxwindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-10-16  Gemma Barson  <gb10@sanger.ac.uk>
 Recalculate coverage after loading features from file
 src/blixemApp/blxwindow.c    | 19 +++++++--
 src/blixemApp/blxwindow.h    | 93 ++++++++++++++++++++++----------------------
 src/blixemApp/coverageview.c | 41 +++++++++----------
 3 files changed, 81 insertions(+), 72 deletions(-)

2012-10-15  Gemma Barson  <gb10@sanger.ac.uk>
 Temp hack to support (invalid) similarity type in gff files
 src/seqtoolsUtils/blxGff3Parser.c | 1 +
 1 file changed, 1 insertion(+)

2012-09-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where reads loaded from a bam file were not displayed
 src/blixemApp/blixem_.h   |  2 +-
 src/blixemApp/blxFetch.c  | 16 ++++++++++------
 src/blixemApp/blxwindow.c |  3 ++-
 3 files changed, 13 insertions(+), 8 deletions(-)

2012-09-24  Gemma Barson  <gb10@sanger.ac.uk>
 Load-file dialog now has the option to enter a URL
 src/blixemApp/blxview.c       | 29 +++++++-------
 src/blixemApp/blxwindow.c     |  5 ++-
 src/seqtoolsUtils/utilities.c | 89 ++++++++++++++++++++++++++++++++++---------
 src/seqtoolsUtils/utilities.h |  2 +-
 4 files changed, 93 insertions(+), 32 deletions(-)

2012-09-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fix some small bugs with load-file dialog
 src/blixemApp/blxFetch.c  |  5 +++--
 src/blixemApp/blxwindow.c | 19 +++++++++++--------
 2 files changed, 14 insertions(+), 10 deletions(-)

2012-09-20  Gemma Barson  <gb10@sanger.ac.uk>
 Allow loading of non-native file formats using fetch methods
 src/blixemApp/blixem_.h           |  11 +-
 src/blixemApp/blxFetch.c          | 162 +++++++++++++++++------------
 src/blixemApp/blxmain.c           |   8 +-
 src/blixemApp/blxview.c           |  24 +++--
 src/blixemApp/blxwindow.c         | 210 +++++++++++++++++++++++++++++++++++++-
 src/dotterApp/dotterMain.c        |   5 +-
 src/seqtoolsUtils/blxGff3Parser.h |  35 ++++---
 src/seqtoolsUtils/blxparser.c     |  10 +-
 src/seqtoolsUtils/blxparser.h     |   2 +-
 src/seqtoolsUtils/utilities.c     |  18 ++++
 src/seqtoolsUtils/utilities.h     |   3 +
 11 files changed, 382 insertions(+), 106 deletions(-)

2012-10-15  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/copy_seq' into develop
2012-10-15  Gemma Barson  <gb10@sanger.ac.uk>
 Warn user if they're about to copy a large amount of text to the clipboard
 src/blixemApp/blxwindow.c | 34 +++++++++++++++++++++++++---------
 src/blixemApp/blxwindow.h |  1 -
 2 files changed, 25 insertions(+), 10 deletions(-)

2012-10-12  Gemma Barson  <gb10@sanger.ac.uk>
 Copy match and reference sequence to clipboard
 src/blixemApp/blxwindow.c  | 846 +++++++++++++++++++++++++--------------------
 src/blixemApp/detailview.c |  48 ++-
 src/blixemApp/detailview.h | 254 +++++++-------
 3 files changed, 647 insertions(+), 501 deletions(-)

2012-10-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fix merge error
 src/blixemApp/blxview.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-10-03  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'develop' into feature/sqlite
2012-10-02  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2012-10-02  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.16' into production
2012-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 Fix Dotter blackout/crash bug if image is too large (RT 266561)
 src/dotterApp/dotplot.c | 50 +++++++++++++++++++------------------------------
 1 file changed, 19 insertions(+), 31 deletions(-)

2012-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 All dotter labels now use the font size from the GTK theme
 src/dotterApp/dotplot.c | 3 +++
 1 file changed, 3 insertions(+)

2012-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug with dotter labels (RT 281848)
 src/dotterApp/dotplot.c | 301 +++++++++++++++++++++++++++++++++++-------------
 src/dotterApp/dotter.c  |   2 +-
 src/dotterApp/dotter_.h |  15 +++
 3 files changed, 234 insertions(+), 84 deletions(-)

2012-09-19  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a harmless bug where duplicate data-types were being created when using the Load GFF File menu
 src/seqtoolsUtils/blxGff3Parser.c | 26 +++++---------------------
 1 file changed, 5 insertions(+), 21 deletions(-)

2012-09-19  Gemma Barson  <gb10@sanger.ac.uk>
 Removed font debug from release version
 src/seqtoolsUtils/utilities.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-09-19  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes for 4.16
 src/doc/User_doc/release_notes.html | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

2012-09-19  Gemma Barson  <gb10@sanger.ac.uk>
 Fix link in About dialog in Dotter and Belvu
 src/belvuApp/belvuWindow.c | 12 ++++++++++++
 src/dotterApp/dotter.c     | 15 ++++++++++++++-
 2 files changed, 26 insertions(+), 1 deletion(-)

2012-09-19  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where Blixem was passing the wrong coords to the fetch command (RT286051)
 src/blixemApp/blxFetch.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2012-09-19  Gemma Barson  <gb10@sanger.ac.uk>
 Add debug for font name
 src/seqtoolsUtils/utilities.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

2012-09-19  Gemma Barson  <gb10@sanger.ac.uk>
 Add alternative name for dejavu font to preferred fonts list
 src/seqtoolsUtils/utilities.c | 1 +
 1 file changed, 1 insertion(+)

2012-09-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where the sequence labels are cut short in Dotter's alignment view
 src/blixemApp/detailview.c     | 2 +-
 src/blixemApp/detailviewtree.c | 6 +++---
 src/dotterApp/alignmenttool.c  | 4 ++--
 src/seqtoolsUtils/utilities.c  | 7 +++++--
 src/seqtoolsUtils/utilities.h  | 2 +-
 5 files changed, 12 insertions(+), 9 deletions(-)

2012-09-07  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where the sequence was being overwritten for optional-fetch
 src/blixemApp/blxFetch.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

2012-08-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fix an issue where the pfetch dialog displays 'not fetched' when sequence data is not actually required
 src/blixemApp/blxFetch.c | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

2012-08-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added cell data functions for generic columns
 src/blixemApp/detailviewtree.c | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

2012-08-21  Gemma Barson  <gb10@sanger.ac.uk>
 Info box now shows all of the feature's fields
 src/blixemApp/blxwindow.c  |  8 +++++--
 src/seqtoolsUtils/blxmsp.c | 59 ++++++++++++++++++++++++++++++++--------------
 2 files changed, 47 insertions(+), 20 deletions(-)

2012-08-20  Gemma Barson  <gb10@sanger.ac.uk>
 Removed some unused functions
 src/blixemApp/detailviewtree.c | 71 +++---------------------------------------
 1 file changed, 4 insertions(+), 67 deletions(-)

2012-08-20  Gemma Barson  <gb10@sanger.ac.uk>
 Make generic text columns sortable
 src/blixemApp/blxview.c    |  3 ++-
 src/blixemApp/blxwindow.c  | 16 +++++++---------
 src/blixemApp/detailview.c | 30 ++----------------------------
 src/seqtoolsUtils/blxmsp.c | 26 ++++++++++++++++++++++----
 src/seqtoolsUtils/blxmsp.h | 15 +++++++++++----
 5 files changed, 44 insertions(+), 46 deletions(-)

2012-08-20  Gemma Barson  <gb10@sanger.ac.uk>
 Add description column
 src/blixemApp/blixem_.h    | 2 +-
 src/blixemApp/blxview.c    | 6 +++++-
 src/seqtoolsUtils/blxmsp.c | 3 ++-
 src/seqtoolsUtils/blxmsp.h | 3 ++-
 4 files changed, 10 insertions(+), 4 deletions(-)

2012-08-20  Gemma Barson  <gb10@sanger.ac.uk>
 Embl tags are now stored in the column info rather than hard-coded
 src/blixemApp/blxFetch.c   | 276 ++++++++++++++++++++++-----------------------
 src/blixemApp/blxview.c    |  32 +++---
 src/seqtoolsUtils/blxmsp.c |  26 ++++-
 src/seqtoolsUtils/blxmsp.h |   9 +-
 4 files changed, 187 insertions(+), 156 deletions(-)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug in sqlite fetch where columns were not being found
 src/blixemApp/blixem_.h    |  4 ++--
 src/blixemApp/blxFetchDb.c | 25 +++++++++++++++++--------
 2 files changed, 19 insertions(+), 10 deletions(-)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where parsed string was not being reset after parsing a field has finished
 src/blixemApp/blxFetch.c | 65 +++++++++++++++++++++---------------------------
 1 file changed, 29 insertions(+), 36 deletions(-)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a crash caused by an uninitialised variable
 src/seqtoolsUtils/blxmsp.c | 1 +
 1 file changed, 1 insertion(+)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying
 src/blixemApp/blxFetch.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Organism column now shows just the abbreviation
 src/blixemApp/detailviewtree.c | 13 ++++++++++---
 src/seqtoolsUtils/blxmsp.c     | 10 ++++++++++
 src/seqtoolsUtils/blxmsp.h     |  2 ++
 3 files changed, 22 insertions(+), 3 deletions(-)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug in filtering whitespace out of parsed embl files
 src/blixemApp/blxFetch.c | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Code refactoring
 src/blixemApp/blxFetch.c | 657 ++++++++++++++++++-----------------------------
 1 file changed, 251 insertions(+), 406 deletions(-)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying
 src/blixemApp/blxFetch.c | 46 +++++++++++++++++++++++-----------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug with optional column data not being saved into the sequence
 src/blixemApp/blxFetch.c   | 50 ++++++++++++++++++++++++++++++++++++++-------
 src/blixemApp/blxwindow.c  |  3 +--
 src/seqtoolsUtils/blxmsp.c | 51 +++++++++++++++++++++++-----------------------
 src/seqtoolsUtils/blxmsp.h |  2 +-
 4 files changed, 70 insertions(+), 36 deletions(-)

2012-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Added a flag in the column info to control which columns are displayed in the mouse-over bar
 src/blixemApp/blxview.c        | 62 ++++++++++++++++++++++--------------------
 src/blixemApp/blxwindow.c      |  4 +--
 src/blixemApp/detailview.c     |  2 +-
 src/blixemApp/detailviewtree.c |  5 +++-
 src/seqtoolsUtils/blxmsp.c     | 60 ++++++++++++++++++++++++----------------
 src/seqtoolsUtils/blxmsp.h     |  5 ++--
 6 files changed, 78 insertions(+), 60 deletions(-)

2012-08-14  Gemma Barson  <gb10@sanger.ac.uk>
 Column values are now stored in an array
 src/blixemApp/blixem_.h              |   2 +-
 src/blixemApp/blxFetch.c             | 206 ++++++++++--------
 src/blixemApp/blxFetchDb.c           |  13 +-
 src/blixemApp/blxdotter.c            |   8 +-
 src/blixemApp/blxview.c              | 125 +++--------
 src/blixemApp/blxwindow.c            |  67 ++----
 src/blixemApp/detailview.c           |  15 +-
 src/blixemApp/detailviewtree.c       |  41 ++--
 src/blixemApp/sequencecellrenderer.c |   6 +-
 src/seqtoolsUtils/blxmsp.c           | 397 +++++++++++++++++++++--------------
 src/seqtoolsUtils/blxmsp.h           |  49 ++---
 11 files changed, 488 insertions(+), 441 deletions(-)

2012-08-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fetch methods for loading optional columns are now specified in the config file
 src/blixemApp/blixem_.h           | 19 +++++-----
 src/blixemApp/blxFetch.c          | 76 ++++++++++++++++++++++++---------------
 src/blixemApp/blxmain.c           |  7 ++--
 src/blixemApp/blxview.c           | 12 +++----
 src/blixemApp/blxwindow.c         | 21 +++++------
 src/seqtoolsUtils/blxGff3Parser.c |  1 +
 src/seqtoolsUtils/blxmsp.c        | 10 +++++-
 src/seqtoolsUtils/blxmsp.h        | 14 ++++----
 8 files changed, 97 insertions(+), 63 deletions(-)

2012-08-13  Gemma Barson  <gb10@sanger.ac.uk>
 Generalise columns code so columns list is no longer hard-coded
 src/blixemApp/blixem_.h           |  67 +++--
 src/blixemApp/blxFetch.c          |  82 +++---
 src/blixemApp/blxmain.c           |   8 +-
 src/blixemApp/blxview.c           | 346 +++++++++++++++++++++-
 src/blixemApp/blxwindow.c         | 100 ++++---
 src/blixemApp/blxwindow.h         |  95 +++---
 src/blixemApp/detailview.c        | 376 ++----------------------
 src/blixemApp/detailview.h        |  28 +-
 src/blixemApp/detailviewtree.c    | 202 +++++++------
 src/dotterApp/dotterMain.c        |   5 +-
 src/seqtoolsUtils/blxGff3Parser.c |   7 +-
 src/seqtoolsUtils/blxGff3Parser.h |   1 +
 src/seqtoolsUtils/blxmsp.c        | 599 ++++++++++++++++++++------------------
 src/seqtoolsUtils/blxmsp.h        |  71 ++++-
 src/seqtoolsUtils/blxparser.c     |  92 ++++--
 src/seqtoolsUtils/blxparser.h     |   2 +-
 src/seqtoolsUtils/utilities.c     |  47 ---
 src/seqtoolsUtils/utilities.h     |   2 -
 18 files changed, 1125 insertions(+), 1005 deletions(-)

2012-08-10  Gemma Barson  <gb10@sanger.ac.uk>
 Make the sort-columns array the same size as the column list
 src/blixemApp/blxwindow.c      |  8 +++++---
 src/blixemApp/detailview.c     | 20 +++++++++++++-------
 src/blixemApp/detailview.h     |  4 ++--
 src/blixemApp/detailviewtree.c | 22 ++++++++++++----------
 4 files changed, 32 insertions(+), 22 deletions(-)

2012-08-10  Gemma Barson  <gb10@sanger.ac.uk>
 Column types are now stored in the column struct
 src/blixemApp/blixem_.h        |  23 +---
 src/blixemApp/detailview.c     |  28 ++++-
 src/blixemApp/detailview.h     | 249 +++++++++++++++++++++--------------------
 src/blixemApp/detailviewtree.c |  25 ++++-
 4 files changed, 173 insertions(+), 152 deletions(-)

2012-08-09  Gemma Barson  <gb10@sanger.ac.uk>
 Rename DetailViewColumnInfo to BlxColumnInfo
 src/blixemApp/blxwindow.c      | 10 ++++-----
 src/blixemApp/detailview.c     | 46 +++++++++++++++++++++---------------------
 src/blixemApp/detailview.h     |  8 ++++----
 src/blixemApp/detailviewtree.c | 10 ++++-----
 4 files changed, 37 insertions(+), 37 deletions(-)

2012-08-09  Gemma Barson  <gb10@sanger.ac.uk>
 Add data type to column info struct
 src/blixemApp/detailview.c | 26 ++++++++++++++------------
 src/blixemApp/detailview.h |  1 +
 2 files changed, 15 insertions(+), 12 deletions(-)

2012-08-08  Gemma Barson  <gb10@sanger.ac.uk>
 Remove usused argument to sequence-fetch functions
 src/blixemApp/blixem_.h        |  4 +-
 src/blixemApp/blxFetch.c       | 91 +++++++++++++-----------------------------
 src/blixemApp/blxFetchDb.c     | 38 +++++++-----------
 src/blixemApp/detailview.c     |  2 +-
 src/blixemApp/detailviewtree.c |  2 +-
 5 files changed, 45 insertions(+), 92 deletions(-)

2012-08-08  Gemma Barson  <gb10@sanger.ac.uk>
 Implement sqlite-fetch for interactively fetching sequences
 src/blixemApp/blixem_.h    |   1 +
 src/blixemApp/blxFetch.c   |  26 +++++----
 src/blixemApp/blxFetchDb.c | 131 +++++++++++++++++++++++++++++++++++++--------
 3 files changed, 126 insertions(+), 32 deletions(-)

2012-08-08  Gemma Barson  <gb10@sanger.ac.uk>
 Hard code the output type for sqlite-fetch
 src/blixemApp/blxFetch.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2012-08-08  Gemma Barson  <gb10@sanger.ac.uk>
 Remove debug code
 src/blixemApp/blxFetchDb.c | 23 ++++++++++++++---------
 src/blixemApp/blxmain.c    |  8 +-------
 2 files changed, 15 insertions(+), 16 deletions(-)

2012-08-08  Gemma Barson  <gb10@sanger.ac.uk>
 Added sqlite fetch code
 src/Makefile.am            |  18 +++-
 src/blixemApp/blixem_.h    |  52 +++++++++-
 src/blixemApp/blxFetch.c   |  51 +++-------
 src/blixemApp/blxFetchDb.c | 230 +++++++++++++++++++++++++++++++++++++++++++++
 src/blixemApp/blxmain.c    |   8 +-
 src/configure.ac           |   8 +-
 src/seqtoolsUtils/blxmsp.c |  44 +++++++++
 src/seqtoolsUtils/blxmsp.h |   1 +
 8 files changed, 363 insertions(+), 49 deletions(-)

2012-09-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where the link in the About dialog did not work
 src/blixemApp/blxwindow.c | 30 ++++++++++++++++++++----------
 1 file changed, 20 insertions(+), 10 deletions(-)

2012-08-31  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2012-08-31  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.15' into production
2012-08-29  Gemma Barson  <gb10@sanger.ac.uk>
 Use cairo for drawing text on dotplot
 src/dotterApp/dotplot.c | 121 ++++++++++++++++++++++++++++--------------------
 1 file changed, 70 insertions(+), 51 deletions(-)

2012-08-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a regression where http-fetch was failing
 src/blixemApp/blxFetch.c | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

2012-08-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a regression where http-fetch was failing
 src/blixemApp/blxFetch.c | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

2012-08-14  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes for 4.15
 src/doc/User_doc/release_notes.html | 11 +++++++++++
 1 file changed, 11 insertions(+)

2012-08-08  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a typo with checking the path of an executable
 src/blixemApp/blxFetch.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-08-03  Gemma Barson  <gb10@sanger.ac.uk>
 Check executables are in the path before trying to call them
 src/belvuApp/belvu.c     | 35 +++++++++++++++++----------
 src/blixemApp/blxFetch.c | 61 +++++++++++++++++++++++++++++++-----------------
 2 files changed, 63 insertions(+), 33 deletions(-)

2012-08-03  Gemma Barson  <gb10@sanger.ac.uk>
 Make sure all stdout messages are flushed
 src/belvuApp/belvu.c           | 118 ++++++++++++++++++++---------------------
 src/belvuApp/belvuAlignment.c  |   6 +--
 src/belvuApp/belvuConsPlot.c   |   8 +--
 src/belvuApp/belvuMain.c       |  26 ++++-----
 src/belvuApp/belvuTree.c       |  84 ++++++++++++++---------------
 src/belvuApp/belvuWindow.c     |  44 +++++++--------
 src/blixemApp/blxFetch.c       |  26 ++++-----
 src/blixemApp/blxmain.c        |  10 ++--
 src/blixemApp/blxview.c        |  10 ++--
 src/blixemApp/blxwindow.c      |  14 ++---
 src/blixemApp/detailview.c     |   4 +-
 src/blixemApp/detailviewtree.c |   6 +--
 src/dotterApp/alignmenttool.c  |   4 +-
 src/dotterApp/dotplot.c        |   6 +--
 src/dotterApp/dotter.c         |   8 +--
 src/dotterApp/dotterMain.c     |   6 +--
 src/seqtoolsUtils/utilities.c  |  46 ++++++----------
 src/seqtoolsUtils/utilities.h  |   7 ++-
 18 files changed, 203 insertions(+), 230 deletions(-)

2012-08-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where the source column is sometimes blank
 src/blixemApp/detailviewtree.c | 43 ++++++++++++++++++++++++++++++++++++------
 1 file changed, 37 insertions(+), 6 deletions(-)

2012-08-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where blixem column label text overlaps
 src/blixemApp/detailview.c    |  2 +-
 src/seqtoolsUtils/utilities.c | 20 ++------------------
 2 files changed, 3 insertions(+), 19 deletions(-)

2012-08-02  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.14' into production
2012-08-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where the 'Load optional data' option was not populating the data correctly
 src/blixemApp/blixem_.h   |  3 +-
 src/blixemApp/blxFetch.c  | 75 +++++++++++++++++++++++++++++++++++++----------
 src/blixemApp/blxview.c   |  2 +-
 src/blixemApp/blxwindow.c |  4 +--
 4 files changed, 64 insertions(+), 20 deletions(-)

2012-07-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a crash when parsing the results from an http fetch
 src/blixemApp/blxFetch.c | 91 ++++++++++++++----------------------------------
 1 file changed, 26 insertions(+), 65 deletions(-)

2012-07-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where the source was not being passed through to the fetch command
 src/blixemApp/blxFetch.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

2012-07-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where bulk-fetching in blixem was not recognising errors in the fetched text
 src/blixemApp/blxFetch.c | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

2012-07-23  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem now ignores leading/trailing whitespace around values in the config file
 src/blixemApp/blxFetch.c      | 14 ++++++++++++--
 src/seqtoolsUtils/utilities.c |  3 ++-
 2 files changed, 14 insertions(+), 3 deletions(-)

2012-07-16  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/styles' into develop
2012-07-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug with setting default UTR colors
 src/blixemApp/blxview.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2012-07-16  Gemma Barson  <gb10@sanger.ac.uk>
 Small comment change
 src/blixemApp/blxmain.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

2012-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 If cds colours are not given in the styles file they are now set to the default colors
 src/blixemApp/blxview.c | 36 +++++++++++++++++++++++-------------
 1 file changed, 23 insertions(+), 13 deletions(-)

2012-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem can now read colors from inherited styles
 src/blixemApp/blixem_.h |  18 +++-
 src/blixemApp/blxmain.c | 270 ++++++++++++++++++++++++++++++++----------------
 2 files changed, 196 insertions(+), 92 deletions(-)

2012-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix potential crash when reading styles file
 src/blixemApp/blxmain.c       | 61 ++++++++++++++++++++++++++++---------------
 src/blixemApp/blxview.c       |  1 -
 src/seqtoolsUtils/utilities.c |  2 --
 3 files changed, 40 insertions(+), 24 deletions(-)

2012-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 The path to the styles file can now be specified in the blixem config file
 src/blixemApp/blixem_.h |  3 ++-
 src/blixemApp/blxmain.c | 18 +++++++++++++++++-
 2 files changed, 19 insertions(+), 2 deletions(-)

2012-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug with setting transparency for styles
 src/blixemApp/blxview.c | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

2012-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Make white colours from the styles file transparent
 src/blixemApp/blxview.c           | 62 ++++++++++++++++++++++++---------------
 src/blixemApp/exonview.c          |  6 ++--
 src/dotterApp/seqtoolsExonView.c  |  6 ++--
 src/seqtoolsUtils/blxGff3Parser.c |  5 ++--
 src/seqtoolsUtils/blxmsp.c        | 43 +++++++++++++++++++--------
 src/seqtoolsUtils/blxmsp.h        |  5 ++--
 6 files changed, 79 insertions(+), 48 deletions(-)

2012-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix error with unrecognised short option
 src/blixemApp/blxmain.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Updated usage docs with new styles file format
 src/blixemApp/blxmain.c           |  48 +++++++------
 src/doc/User_doc/blixem_usage.txt | 139 ++++++++++++++++++++++----------------
 2 files changed, 106 insertions(+), 81 deletions(-)

2012-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem can now read colors from a zmap styles file
 src/blixemApp/blxmain.c | 158 +++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 129 insertions(+), 29 deletions(-)

2012-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Reorganise styles file code
 src/blixemApp/blxmain.c | 67 ++++++++++++++++++++++++++++++++++---------------
 1 file changed, 47 insertions(+), 20 deletions(-)

2012-07-10  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/config' into develop
2012-07-10  Gemma Barson  <gb10@sanger.ac.uk>
 Updated test plan
 src/test/test_plan.ods | Bin 38241 -> 38902 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2012-07-10  Gemma Barson  <gb10@sanger.ac.uk>
 Improved error handling
 src/blixemApp/blxFetch.c          | 333 ++++++++++++++++++++++++--------------
 src/seqtoolsUtils/blxGff3Parser.c |   4 +-
 src/seqtoolsUtils/utilities.c     |  15 +-
 src/seqtoolsUtils/utilities.h     |   2 +-
 4 files changed, 226 insertions(+), 128 deletions(-)

2012-07-09  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying
 src/blixemApp/blixem_.h  |   2 +-
 src/blixemApp/blxFetch.c | 212 +++++++++++++++++++++++++++--------------------
 2 files changed, 123 insertions(+), 91 deletions(-)

2012-07-09  Gemma Barson  <gb10@sanger.ac.uk>
 Local config file now overrides command-line config file
 src/blixemApp/blixem_.h       |   2 +-
 src/blixemApp/blxFetch.c      | 179 +++++++++++++++++++++++-------------------
 src/blixemApp/blxmain.c       |   5 +-
 src/blixemApp/blxview.c       |  13 ++-
 src/seqtoolsUtils/utilities.c |  40 +++++-----
 5 files changed, 127 insertions(+), 112 deletions(-)

2012-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2012-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'hotfix/4.13.3' into production
2012-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Make dotter use internal sequence rather than trying to fetch it
 src/blixemApp/blxdotter.c | 5 -----
 1 file changed, 5 deletions(-)

2012-07-02  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

2012-07-02  Gemma Barson  <gb10@sanger.ac.uk>
 Add new keyboard shortcuts to belvu docs
 src/doc/User_doc/Belvu_manual.odt       | Bin 970098 -> 970146 bytes
 src/doc/User_doc/Belvu_manual.pdf       | Bin 819755 -> 819868 bytes
 src/doc/User_doc/belvu_quick_start.html | 122 +++++++++++++++++---------------
 3 files changed, 66 insertions(+), 56 deletions(-)

2012-07-02  Gemma Barson  <gb10@sanger.ac.uk>
 Add Belvu keyboard shortcuts
 src/belvuApp/belvuWindow.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

2012-06-26  Gemma Barson  <gb10@sanger.ac.uk>
 Allow user to cancel fetch dialog if fetch hangs
 src/blixemApp/blxFetch.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2012-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Catch segv faults and print backtrace
 src/blixemApp/blxmain.c       |  4 ++++
 src/seqtoolsUtils/utilities.c | 21 +++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |  2 ++
 3 files changed, 27 insertions(+)

2012-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fix an error that can occur when opening firefox
 src/seqtoolsUtils/seqtoolsWebBrowser.c | 1 +
 1 file changed, 1 insertion(+)

2012-06-27  Ed Griffiths  <edgrif@sanger.ac.uk>
 "minor comment change"
 src/README | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2012-06-19  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a compile error where libpfetch was being compiled even if libcurl not available
 src/Makefile.am | 4 ++++
 1 file changed, 4 insertions(+)

2012-06-19  Gemma Barson  <gb10@sanger.ac.uk>
 Change config file separator to ';' to be consistent with zmap
 src/seqtoolsUtils/utilities.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2012-06-18  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into release/4.14
2012-06-18  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'hotfix/4.13.2' into production
2012-06-18  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

2012-06-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fix compilation error on Ubuntu 12.02
 src/Makefile.am | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

2012-06-15  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes for 4.14
 src/doc/User_doc/release_notes.html | 8 ++++++++
 1 file changed, 8 insertions(+)

2012-06-15  Gemma Barson  <gb10@sanger.ac.uk>
 Updated user manual with new config file instructions
 src/doc/User_doc/Blixem_manual.odt | Bin 994719 -> 998860 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 766962 -> 778696 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2012-06-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where fetch was not re-tried after socket fetch fails
 src/blixemApp/blxFetch.c | 50 ++++++++++++++++++++++++------------------------
 1 file changed, 25 insertions(+), 25 deletions(-)

2012-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/config' into develop
2012-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Add 'raw' output type and distinguish this from 'fasta'
 src/blixemApp/blixem_.h  |  1 +
 src/blixemApp/blxFetch.c | 94 ++++++++++++++++++++++++------------------------
 2 files changed, 49 insertions(+), 46 deletions(-)

2012-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying
 src/blixemApp/blxFetch.c | 404 +++++++++++++++++------------------------------
 1 file changed, 145 insertions(+), 259 deletions(-)

2012-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug with checking the fetch error string
 src/blixemApp/blxFetch.c | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

2012-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Remove hard-coded 'no match' and 'not authorized' checks
 src/blixemApp/blxFetch.c | 98 ++++++++++++++++++++++++++++++++----------------
 1 file changed, 66 insertions(+), 32 deletions(-)

2012-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Read expected error messages from fetch config
 src/blixemApp/blixem_.h       |  2 ++
 src/blixemApp/blxFetch.c      | 53 +++++++------------------------------------
 src/seqtoolsUtils/utilities.c | 39 +++++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |  2 ++
 4 files changed, 51 insertions(+), 45 deletions(-)

2012-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix an issue where re-trying after http fetch would pop up a second window
 src/blixemApp/blixem_.h        |  2 +-
 src/blixemApp/blxFetch.c       | 83 ++++++++++++++++++++++++++----------------
 src/blixemApp/detailview.c     |  2 +-
 src/blixemApp/detailviewtree.c |  2 +-
 src/seqtoolsUtils/utilities.c  | 52 +++++++++++++++++---------
 src/seqtoolsUtils/utilities.h  |  2 +-
 6 files changed, 90 insertions(+), 53 deletions(-)

2012-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 Dotter no longer fetches sequence data
 src/blixemApp/blxdotter.c | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

2012-06-12  Gemma Barson  <gb10@sanger.ac.uk>
 Remove delimiters from fetch method config values
 src/blixemApp/blxFetch.c | 119 ++++++++++++++++++++++++++++++++---------------
 1 file changed, 82 insertions(+), 37 deletions(-)

2012-06-12  Gemma Barson  <gb10@sanger.ac.uk>
 Remove incorrect dependency on data type for fetching optional data
 src/seqtoolsUtils/blxmsp.c | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

2012-06-12  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/config' into develop
2012-06-12  Gemma Barson  <gb10@sanger.ac.uk>
 Add a separator field to the config for separating lists of sequence names to fetch
 src/blixemApp/blixem_.h   | 4 +++-
 src/blixemApp/blxFetch.c  | 6 +++++-
 src/libpfetch/libpfetch.c | 5 ++---
 3 files changed, 10 insertions(+), 5 deletions(-)

2012-06-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug with default methods not being used
 src/seqtoolsUtils/blxmsp.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2012-06-12  Gemma Barson  <gb10@sanger.ac.uk>
 Remove unused pfetch fields
 src/blixemApp/blxFetch.c | 25 +++----------------------
 1 file changed, 3 insertions(+), 22 deletions(-)

2012-06-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bugs with new config for http fetch
 src/blixemApp/blixem_.h   |   8 +-
 src/blixemApp/blxFetch.c  | 312 +++++++++++++++++++++++++++++++++-------------
 src/libpfetch/libpfetch.c |  73 ++---------
 3 files changed, 242 insertions(+), 151 deletions(-)

2012-06-12  Gemma Barson  <gb10@sanger.ac.uk>
 Small improvement to error message
 src/blixemApp/blxFetch.c | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2012-06-12  Gemma Barson  <gb10@sanger.ac.uk>
 Add optional file tag to GFF and config file
 src/blixemApp/blxFetch.c          |  7 +++++++
 src/seqtoolsUtils/blxGff3Parser.c | 34 +++++++++++++++++++++++++++++++++-
 src/seqtoolsUtils/blxmsp.c        |  6 ++++--
 src/seqtoolsUtils/blxmsp.h        |  5 +++--
 src/seqtoolsUtils/blxparser.c     | 12 ++++++------
 5 files changed, 53 insertions(+), 11 deletions(-)

2012-06-11  Gemma Barson  <gb10@sanger.ac.uk>
 Remove unused 'url' field in MSP struct
 src/seqtoolsUtils/blxGff3Parser.c | 14 +-------------
 src/seqtoolsUtils/blxmsp.c        |  9 ++-------
 src/seqtoolsUtils/blxmsp.h        |  2 +-
 src/seqtoolsUtils/blxparser.c     | 12 ++++++------
 4 files changed, 10 insertions(+), 27 deletions(-)

2012-06-11  Gemma Barson  <gb10@sanger.ac.uk>
 Add source to substitution variables
 src/blixemApp/blxFetch.c | 5 +++++
 1 file changed, 5 insertions(+)

2012-06-11  Gemma Barson  <gb10@sanger.ac.uk>
 Implement internal fetch mode
 src/blixemApp/blixem_.h  |  4 ++-
 src/blixemApp/blxFetch.c | 76 ++++++++++++++++++++++++++++++++++++++++++------
 2 files changed, 70 insertions(+), 10 deletions(-)

2012-06-01  Gemma Barson  <gb10@sanger.ac.uk>
 Provide a utility to get the fetch output type as a string
 src/blixemApp/blixem_.h  |   9 ++-
 src/blixemApp/blxFetch.c | 147 +++++++++++++++++++++++++++++++----------------
 2 files changed, 103 insertions(+), 53 deletions(-)

2012-06-01  Gemma Barson  <gb10@sanger.ac.uk>
 Move all fetch code to blxFetch.c
 src/blixemApp/blxFetch.c | 828 +++++++++++++++++++++++++++++++++++++++--------
 src/blixemApp/blxview.c  | 552 -------------------------------
 2 files changed, 691 insertions(+), 689 deletions(-)

2012-06-01  Gemma Barson  <gb10@sanger.ac.uk>
 Provide utility to get fetch mode as string
 src/blixemApp/blixem_.h  | 11 ++---------
 src/blixemApp/blxFetch.c | 45 +++++++++++++++++++++++++++++++++++++--------
 2 files changed, 39 insertions(+), 17 deletions(-)

2012-06-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a crash that happens if there is no config file
 src/seqtoolsUtils/blxGff3Parser.c | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

2012-05-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where features were not being linked under the same parent correctly
 src/seqtoolsUtils/blxmsp.c | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

2012-05-31  Gemma Barson  <gb10@sanger.ac.uk>
 Add error handling for bad fetch commands
 src/blixemApp/blixem_.h  |   2 +-
 src/blixemApp/blxFetch.c |  90 ++++++++++++++++++++++++++++++-----------
 src/blixemApp/blxview.c  | 102 +++++++++++++++++++++++++++--------------------
 3 files changed, 125 insertions(+), 69 deletions(-)

2012-05-30  Gemma Barson  <gb10@sanger.ac.uk>
 Add link-features-by-name option to config file
 src/blixemApp/blixem_.h           |  5 ++-
 src/blixemApp/blxFetch.c          | 27 ++++++------
 src/blixemApp/blxview.c           |  2 +-
 src/blixemApp/blxwindow.c         |  3 +-
 src/dotterApp/dotterMain.c        |  2 +-
 src/seqtoolsUtils/blxGff3Parser.c | 34 ++++++++++++++-
 src/seqtoolsUtils/blxmsp.c        | 87 ++++++++++++++++++++++++---------------
 src/seqtoolsUtils/blxmsp.h        | 12 ++++--
 src/seqtoolsUtils/blxparser.c     | 12 +++---
 9 files changed, 121 insertions(+), 63 deletions(-)

2012-05-30  Gemma Barson  <gb10@sanger.ac.uk>
 Improve error handling when reading config file
 src/blixemApp/blxFetch.c      | 7 ++++++-
 src/seqtoolsUtils/blxmsp.c    | 2 +-
 src/seqtoolsUtils/utilities.c | 6 ++----
 3 files changed, 9 insertions(+), 6 deletions(-)

2012-05-30  Gemma Barson  <gb10@sanger.ac.uk>
 Improve error handling when setting up sockets
 src/blixemApp/blxFetch.c | 130 ++++++++++++++++++++++++++---------------------
 1 file changed, 73 insertions(+), 57 deletions(-)

2012-05-30  Gemma Barson  <gb10@sanger.ac.uk>
 New fetch code now supports the old default-pfetch-method key for backwards compatibility
 src/blixemApp/blxFetch.c | 5 +++++
 1 file changed, 5 insertions(+)

2012-05-30  Gemma Barson  <gb10@sanger.ac.uk>
 Remove unused variable
 src/seqtoolsUtils/utilities.c | 2 --
 1 file changed, 2 deletions(-)

2012-05-29  Gemma Barson  <gb10@sanger.ac.uk>
 Fix rebase error; wrong type used for utility function
 src/seqtoolsUtils/utilities.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a spurious error message when fetch method is 'none'
 src/blixemApp/blxFetch.c | 6 ++++++
 1 file changed, 6 insertions(+)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix misleading function name
 src/blixemApp/blxview.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where default fetch method list was being used even though custom fetch method list had been set
 src/seqtoolsUtils/blxmsp.c | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Check the output type is valid for command-fetch methods
 src/blixemApp/blxview.c | 40 ++++++++++++++++++++++++++++++++++++----
 1 file changed, 36 insertions(+), 4 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bug with appending null string to fetch command
 src/blixemApp/blxFetch.c | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Better user message text
 src/blixemApp/blxFetch.c | 2 +-
 src/blixemApp/blxview.c  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a rebase error; wrong type returned from utility function
 src/seqtoolsUtils/utilities.c | 9 +++------
 src/seqtoolsUtils/utilities.h | 2 +-
 2 files changed, 4 insertions(+), 7 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix an issue where blixem would try to fetch data not relevant to the fetch method used
 src/blixemApp/blxFetch.c |  2 +-
 src/blixemApp/blxview.c  | 84 +++++++++++++++++++++++++++++++++++++-----------
 2 files changed, 66 insertions(+), 20 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug with fetching using secondary fetch methods
 src/blixemApp/blxFetch.c   |  2 +-
 src/blixemApp/blxview.c    | 16 +++++++++++-----
 src/seqtoolsUtils/blxmsp.c |  4 ++--
 3 files changed, 14 insertions(+), 8 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 Variation urls are now specified in config
 src/blixemApp/detailview.c           |   23 +-
 src/test/data/chr4_dna_align.gff     | 2366 +++++++++++++++++-----------------
 src/test/data/chr4_protein_align.gff | 2366 +++++++++++++++++-----------------
 3 files changed, 2369 insertions(+), 2386 deletions(-)

2012-05-28  Gemma Barson  <gb10@sanger.ac.uk>
 New config fetch methods now mostly working
 src/blixemApp/blixem_.h            | 224 +++++-----
 src/blixemApp/blxFetch.c           | 866 +++++++++++++++++++++----------------
 src/blixemApp/blxdotter.c          | 118 +----
 src/blixemApp/blxmain.c            |  10 +-
 src/blixemApp/blxview.c            | 596 +++++++++++--------------
 src/blixemApp/blxwindow.c          |  27 +-
 src/blixemApp/blxwindow.h          |   2 -
 src/blixemApp/detailviewtree.c     |   9 +-
 src/libpfetch/libpfetch-cmarshal.c |   6 +-
 src/libpfetch/libpfetch-cmarshal.h |   4 +-
 src/seqtoolsUtils/blxGff3Parser.c  |  12 +-
 src/seqtoolsUtils/blxmsp.c         |  44 +-
 src/seqtoolsUtils/blxmsp.h         |  21 +-
 src/seqtoolsUtils/utilities.c      |  33 ++
 src/seqtoolsUtils/utilities.h      |   2 +
 15 files changed, 966 insertions(+), 1008 deletions(-)

2012-05-16  Gemma Barson  <gb10@sanger.ac.uk>
 WIP
 src/blixemApp/blixem_.h   |  35 ++++++++++----
 src/blixemApp/blxFetch.c  | 116 ++++++++++++++++++++++++++++++++++++++--------
 src/blixemApp/blxwindow.c |   8 +---
 3 files changed, 123 insertions(+), 36 deletions(-)

2012-05-15  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: generalise fetch methods
 src/blixemApp/blixem_.h           | 102 ++++---
 src/blixemApp/blxFetch.c          | 583 +++++++-------------------------------
 src/blixemApp/blxdotter.c         |   2 +-
 src/blixemApp/blxmain.c           |   7 +-
 src/blixemApp/blxview.c           |  71 ++---
 src/blixemApp/blxwindow.c         |  43 ++-
 src/blixemApp/blxwindow.h         |   1 -
 src/blixemApp/detailviewtree.c    |   9 +-
 src/seqtoolsUtils/blxGff3Parser.c |  63 ++--
 src/seqtoolsUtils/blxmsp.c        |  47 ++-
 src/seqtoolsUtils/blxmsp.h        |  22 +-
 11 files changed, 323 insertions(+), 627 deletions(-)

2012-05-31  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2012-05-31  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'hotfix/4.13.1' into production
2012-05-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where features were not being linked under the same parent correctly
 src/seqtoolsUtils/blxmsp.c | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

2012-05-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where features were not being linked under the same parent correctly
 src/seqtoolsUtils/blxmsp.c | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

2012-05-29  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2012-05-29  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.13' into production
2012-05-29  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

2012-05-24  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dotter_crash' into develop
2012-05-17  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: Fix a crash for long, skinny plots
 src/dotterApp/dotplot.c | 29 ++++++++++++++++++++++++-----
 1 file changed, 24 insertions(+), 5 deletions(-)

2012-05-18  Gemma Barson  <gb10@sanger.ac.uk>
 If fetch fails, display stored sequence data instead
 src/blixemApp/blixem_.h        |   2 +-
 src/blixemApp/blxFetch.c       |  90 ++++++++++++++++++----------
 src/blixemApp/detailviewtree.c |   3 +-
 src/seqtoolsUtils/blxmsp.c     |  14 +++++
 src/seqtoolsUtils/blxmsp.h     | 129 +++++++++++++++++++++--------------------
 src/seqtoolsUtils/utilities.c  |  21 ++++---
 src/seqtoolsUtils/utilities.h  |   2 +-
 7 files changed, 154 insertions(+), 107 deletions(-)

2012-05-18  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem no longer quits if you cancel the sequence fetch
 src/blixemApp/blxview.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2012-05-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where the squash-matches command-line argument was being overriden by the saved settings
 src/blixemApp/blxwindow.c | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

2012-05-02  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2012-04-30  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.12' into production
2012-04-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with printing labels in dotter alignment tool
 src/blixemApp/detailview.c     |   7 -
 src/blixemApp/detailviewtree.c |  29 ++--
 src/dotterApp/alignmenttool.c  |   6 +-
 src/seqtoolsUtils/utilities.c  |  39 ++++-
 src/seqtoolsUtils/utilities.h  | 328 +++++++++++++++++++++--------------------
 5 files changed, 217 insertions(+), 192 deletions(-)

2012-04-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a bug where Ctrl-P printed the wrong window when called from the alignment tool
 src/dotterApp/dotter.c | 23 -----------------------
 1 file changed, 23 deletions(-)

2012-04-25  Gemma Barson  <gb10@sanger.ac.uk>
 Alignment tool now has white background when printed
 src/dotterApp/alignmenttool.c | 27 ++++++++++++++++++++++-----
 1 file changed, 22 insertions(+), 5 deletions(-)

2012-04-25  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dotter_select' into develop
2012-04-25  Gemma Barson  <gb10@sanger.ac.uk>
 Make sure the primary buffer is not overwritten accidentally
 src/dotterApp/alignmenttool.c | 6 ++++++
 1 file changed, 6 insertions(+)

2012-04-25  Gemma Barson  <gb10@sanger.ac.uk>
 Removed debug output
 src/dotterApp/alignmenttool.c | 4 ----
 1 file changed, 4 deletions(-)

2012-04-24  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying
 src/dotterApp/alignmenttool.c | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

2012-04-24  Gemma Barson  <gb10@sanger.ac.uk>
 Make sure we don't index out of range in case of bad coords
 src/dotterApp/alignmenttool.c | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

2012-04-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with sequence selection for reverse strand and offet sequences
 src/dotterApp/alignmenttool.c | 130 ++++++++++++++++++++++++++++++++----------
 src/dotterApp/dotter.c        |  30 ++++++++++
 src/dotterApp/dotter_.h       |  87 ++++++++++++++--------------
 3 files changed, 175 insertions(+), 72 deletions(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Added menu item for 'clear selection'
 src/dotterApp/alignmenttool.c | 44 ++++++++++++-------------------------------
 1 file changed, 12 insertions(+), 32 deletions(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue with highlighting multiple sequences
 src/dotterApp/alignmenttool.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Improved menu items for selections
 src/dotterApp/alignmenttool.c | 76 ++++++++++++++++++++-----------------------
 1 file changed, 35 insertions(+), 41 deletions(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Added menu item to copy selection coords
 src/dotterApp/alignmenttool.c | 65 +++++++++++++++++++++++++++++++++++--------
 1 file changed, 53 insertions(+), 12 deletions(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Copying coords in dotter now places them on the primary clipboard
 src/dotterApp/alignmenttool.c | 10 ++++++++++
 1 file changed, 10 insertions(+)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Escape key now cancels text selection
 src/dotterApp/alignmenttool.c | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Ctrl-C now copies selected text to default clipboard
 src/dotterApp/alignmenttool.c | 54 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with double-click selection
 src/dotterApp/alignmenttool.c | 42 ++++++++++++++++++++++++------------------
 1 file changed, 24 insertions(+), 18 deletions(-)

2012-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Double-click highlights visibile sequence
 src/dotterApp/alignmenttool.c | 101 ++++++++++++++++++++++++++++++++++--------
 1 file changed, 83 insertions(+), 18 deletions(-)

2012-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Selected sequence is now highlighted
 src/dotterApp/alignmenttool.c | 292 ++++++++++++++++++++++++++----------------
 1 file changed, 185 insertions(+), 107 deletions(-)

2012-04-19  Gemma Barson  <gb10@sanger.ac.uk>
 Selected text is now placed on primary clipboard
 src/dotterApp/alignmenttool.c | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

2012-04-19  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: selecting sequence in dotter
 src/dotterApp/alignmenttool.c | 117 ++++++++++++++++++++++++++++++++++--------
 1 file changed, 97 insertions(+), 20 deletions(-)

2012-04-19  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: select sequence from the alignment tool in dotter
 src/dotterApp/alignmenttool.c | 403 ++++++++++++++++++++++++++++--------------
 1 file changed, 269 insertions(+), 134 deletions(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Added more dotter example cases
 src/examples/Q9H8G1.fasta                  |  1 +
 src/examples/README                        | 12 +++++++++---
 src/examples/chr4_translation_frame1.fasta |  1 +
 3 files changed, 11 insertions(+), 3 deletions(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a problem with the background color after printing
 src/dotterApp/dotter.c | 865 +++++++++++++++++++++++++------------------------
 1 file changed, 437 insertions(+), 428 deletions(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fix bad coords in the rev strand when the alignment tool length is even
 src/dotterApp/alignmenttool.c | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

2012-04-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression where the greyramp tool had the wrong context menu
 src/dotterApp/greyramptool.c | 3 ---
 1 file changed, 3 deletions(-)

2012-04-12  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

2012-04-12  Gemma Barson  <gb10@sanger.ac.uk>
 Removed duplicate sequence data from the sample gff files
 src/test/data/chr4_dna_align.gff     |  908 ++---
 src/test/data/chr4_protein_align.gff | 6062 +++++++++++++++++-----------------
 2 files changed, 3485 insertions(+), 3485 deletions(-)

2012-04-10  Gemma Barson  <gb10@sanger.ac.uk>
 Updated copyright notices to 2012
 src/belvuApp/belvu.c                   | 9 +--------
 src/belvuApp/belvuAlignment.c          | 2 +-
 src/belvuApp/belvuAlignment.h          | 2 +-
 src/belvuApp/belvuConsPlot.c           | 2 +-
 src/belvuApp/belvuConsPlot.h           | 2 +-
 src/belvuApp/belvuMain.c               | 2 +-
 src/belvuApp/belvuTree.c               | 2 +-
 src/belvuApp/belvuTree.h               | 4 ++--
 src/belvuApp/belvuWindow.c             | 2 +-
 src/belvuApp/belvuWindow.h             | 2 +-
 src/belvuApp/belvu_.h                  | 2 +-
 src/blixemApp/bigpicture.c             | 2 +-
 src/blixemApp/bigpicture.h             | 2 +-
 src/blixemApp/bigpicturegrid.c         | 2 +-
 src/blixemApp/bigpicturegrid.h         | 2 +-
 src/blixemApp/blixem_.h                | 2 +-
 src/blixemApp/blxFetch.c               | 2 +-
 src/blixemApp/blxdotter.c              | 2 +-
 src/blixemApp/blxdotter.h              | 2 +-
 src/blixemApp/blxmain.c                | 2 +-
 src/blixemApp/blxview.c                | 2 +-
 src/blixemApp/blxview.h                | 2 +-
 src/blixemApp/blxwindow.c              | 2 +-
 src/blixemApp/blxwindow.h              | 2 +-
 src/blixemApp/coverageview.c           | 2 +-
 src/blixemApp/coverageview.h           | 4 ++--
 src/blixemApp/detailview.c             | 2 +-
 src/blixemApp/detailview.h             | 2 +-
 src/blixemApp/detailviewtree.c         | 2 +-
 src/blixemApp/detailviewtree.h         | 2 +-
 src/blixemApp/exonview.c               | 2 +-
 src/blixemApp/exonview.h               | 2 +-
 src/blixemApp/sequencecellrenderer.c   | 2 +-
 src/blixemApp/sequencecellrenderer.h   | 2 +-
 src/dotterApp/alignmenttool.c          | 2 +-
 src/dotterApp/dotplot.c                | 2 +-
 src/dotterApp/dotter.c                 | 2 +-
 src/dotterApp/dotter.h                 | 2 +-
 src/dotterApp/dotterKarlin.c           | 2 +-
 src/dotterApp/dotterMain.c             | 2 +-
 src/dotterApp/dotter_.h                | 2 +-
 src/dotterApp/greyramptool.c           | 2 +-
 src/dotterApp/seqtoolsExonView.c       | 2 +-
 src/dotterApp/seqtoolsExonView.h       | 2 +-
 src/libpfetch/libcurlobject.c          | 2 +-
 src/libpfetch/libcurlobject.h          | 2 +-
 src/libpfetch/libcurlobject_I.h        | 2 +-
 src/libpfetch/libpfetch-utils.c        | 2 +-
 src/libpfetch/libpfetch.c              | 2 +-
 src/libpfetch/libpfetch.h              | 2 +-
 src/libpfetch/libpfetch_I.h            | 2 +-
 src/libpfetch/libpfetch_P.h            | 2 +-
 src/seqtoolsUtils/blxGff3Parser.c      | 2 +-
 src/seqtoolsUtils/blxGff3Parser.h      | 2 +-
 src/seqtoolsUtils/blxmsp.c             | 2 +-
 src/seqtoolsUtils/blxmsp.h             | 2 +-
 src/seqtoolsUtils/blxparser.c          | 2 +-
 src/seqtoolsUtils/blxparser.h          | 2 +-
 src/seqtoolsUtils/iupac.h              | 2 +-
 src/seqtoolsUtils/seqtoolsWebBrowser.c | 2 +-
 src/seqtoolsUtils/translate.c          | 2 +-
 src/seqtoolsUtils/utilities.c          | 2 +-
 src/seqtoolsUtils/utilities.h          | 2 +-
 src/seqtoolsUtils/version.h            | 2 +-
 64 files changed, 66 insertions(+), 73 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Inlcude examples directory in the distribution
 src/Makefile.am | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Revert "Fix a regression where matches were misaligned due to problems reading the cigar string""
 src/seqtoolsUtils/blxGff3Parser.c | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Revert "Updated release notes""
 src/doc/User_doc/release_notes.html | 12 ++++++++++++
 1 file changed, 12 insertions(+)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Revert "Merge branch 'feature/cigar' into develop""
 src/blixemApp/blixem_.h           |   2 +-
 src/blixemApp/blxFetch.c          |  28 +++---
 src/blixemApp/blxview.c           |   5 +-
 src/blixemApp/blxwindow.c         |  19 +++-
 src/blixemApp/detailview.c        |   9 +-
 src/blixemApp/detailviewtree.c    |  27 ++++--
 src/dotterApp/dotterMain.c        |   2 +-
 src/seqtoolsUtils/blxGff3Parser.c |  74 ++++++++++++---
 src/seqtoolsUtils/blxmsp.c        | 189 +++++++++++++++++++++++++++-----------
 src/seqtoolsUtils/blxmsp.h        |   3 +-
 src/seqtoolsUtils/utilities.c     |   6 +-
 11 files changed, 262 insertions(+), 102 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Revert "Fixed a refresh problem when selecting variations""
 src/blixemApp/blxwindow.c      |  3 +--
 src/blixemApp/detailview.c     | 15 +++++++++------
 src/blixemApp/detailview.h     |  2 +-
 src/blixemApp/detailviewtree.c |  3 +--
 4 files changed, 12 insertions(+), 11 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Revert "Fixed a bug in protein blixem where you could not select a feature in the variations track""
 src/blixemApp/detailview.c | 1379 ++++++++++++++++++++++++--------------------
 src/blixemApp/detailview.h |    5 +-
 2 files changed, 749 insertions(+), 635 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Revert "Fixed a typo on the Settings dialog (RT:254611)""
 src/blixemApp/blxwindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'hotfix/4.10.1' into production
2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Fixed a typo on the Settings dialog (RT:254611)"
 src/blixemApp/blxwindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Fixed a bug in protein blixem where you could not select a feature in the variations track"
 src/blixemApp/detailview.c | 1379 ++++++++++++++++++++------------------------
 src/blixemApp/detailview.h |    5 +-
 2 files changed, 635 insertions(+), 749 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Fixed a refresh problem when selecting variations"
 src/blixemApp/blxwindow.c      |  3 ++-
 src/blixemApp/detailview.c     | 15 ++++++---------
 src/blixemApp/detailview.h     |  2 +-
 src/blixemApp/detailviewtree.c |  3 ++-
 4 files changed, 11 insertions(+), 12 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Merge branch 'feature/cigar' into develop"
 src/blixemApp/blixem_.h           |   2 +-
 src/blixemApp/blxFetch.c          |  28 +++---
 src/blixemApp/blxview.c           |   5 +-
 src/blixemApp/blxwindow.c         |  19 +---
 src/blixemApp/detailview.c        |   9 +-
 src/blixemApp/detailviewtree.c    |  27 ++----
 src/dotterApp/dotterMain.c        |   2 +-
 src/seqtoolsUtils/blxGff3Parser.c |  74 +++------------
 src/seqtoolsUtils/blxmsp.c        | 189 +++++++++++---------------------------
 src/seqtoolsUtils/blxmsp.h        |   3 +-
 src/seqtoolsUtils/utilities.c     |   6 +-
 11 files changed, 102 insertions(+), 262 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Updated release notes"
 src/doc/User_doc/release_notes.html | 12 ------------
 1 file changed, 12 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Revert "Fix a regression where matches were misaligned due to problems reading the cigar string"
 src/seqtoolsUtils/blxGff3Parser.c | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Added examples directory
 src/README                            |  4 +++-
 src/doc/User_doc/release_notes.html   | 11 +++++++++++
 src/examples/DA730641.fasta           |  1 +
 src/examples/PF02171_seed.stock       |  1 +
 src/examples/README                   | 18 ++++++++++++++++++
 src/examples/chr4_dna_align.gff       |  1 +
 src/examples/chr4_protein_align.gff   |  1 +
 src/examples/chr4_ref_seq.fasta       |  1 +
 src/examples/chr4_ref_seq_short.fasta |  1 +
 9 files changed, 38 insertions(+), 1 deletion(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Small update to test README doc
 src/test/README | 1 +
 1 file changed, 1 insertion(+)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed incorrect return value from blixem
 src/belvuApp/belvuMain.c   | 2 +-
 src/blixemApp/blxmain.c    | 3 +--
 src/dotterApp/dotterMain.c | 2 +-
 3 files changed, 3 insertions(+), 4 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Updated test scripts README
 src/test/README | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Added some simple automated blixem tests
 src/test/scripts/automated/blixem/test1         |  26 +++
 src/test/scripts/automated/blixem/test1_results | 207 ++++++++++++++++++++++++
 src/test/scripts/automated/blixem/test2         |  26 +++
 src/test/scripts/automated/blixem/test2_results | 123 ++++++++++++++
 4 files changed, 382 insertions(+)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to belvu automated tests
 src/test/scripts/automated/belvu/test1          | 23 +++++++++++++++++++++--
 src/test/scripts/automated/belvu/test10         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test11         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test12         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test13         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test14         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test15         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test16         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test17         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test18         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test19         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test1_results  |  2 +-
 src/test/scripts/automated/belvu/test2          | 23 +++++++++++++++++++++--
 src/test/scripts/automated/belvu/test20         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test21         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test21_results |  2 +-
 src/test/scripts/automated/belvu/test22         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test23         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test24         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test25         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test26         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test26_results |  2 +-
 src/test/scripts/automated/belvu/test27         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test27_results |  2 +-
 src/test/scripts/automated/belvu/test28         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test29         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test3          | 23 +++++++++++++++++++++--
 src/test/scripts/automated/belvu/test30         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test31         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test32         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test33         | 22 +++++++++++++++++++++-
 src/test/scripts/automated/belvu/test34         | 22 +++++++++++++++++++++-
 src/test/scripts/automated/belvu/test35         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test36         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test37         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test38         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test39         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test4          | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test40         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test41         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test42         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test43         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test44         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test45         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test46         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test47         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test48         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test49         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test5          | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test50         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test51         | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test6          | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test7          | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test8          | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test9          | 24 ++++++++++++++++++++++--
 src/test/scripts/automated/belvu/test9_results  |  2 +-
 56 files changed, 1122 insertions(+), 105 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to dotter tests
 src/test/scripts/automated/dotter/test1            |  25 ++++++++++++-
 src/test/scripts/automated/dotter/test1_result.dot | Bin 460197 -> 0 bytes
 src/test/scripts/automated/dotter/test1_results    | Bin 0 -> 455204 bytes
 src/test/scripts/automated/dotter/test2            |  26 ++++++++++++-
 .../dotter/{test2_result.pdf => test2_results}     | Bin
 src/test/scripts/automated/dotter/test3            |  41 ++++++++++++++++++++-
 src/test/scripts/automated/dotter/test3_result.dot | Bin 460197 -> 0 bytes
 .../scripts/automated/dotter/test3_results.dot     | Bin 0 -> 455204 bytes
 .../dotter/{test3_result.pdf => test3_results.pdf} | Bin
 9 files changed, 86 insertions(+), 6 deletions(-)

2012-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to manual tests
 src/test/scripts/manual/belvu/test1  | 19 +++++++++++++++++--
 src/test/scripts/manual/belvu/test2  | 20 ++++++++++++++++++--
 src/test/scripts/manual/belvu/test3  | 23 +++++++++++++++++++++--
 src/test/scripts/manual/belvu/test4  | 18 ++++++++++++++++--
 src/test/scripts/manual/belvu/test5  | 20 ++++++++++++++++++--
 src/test/scripts/manual/blixem/test1 | 19 +++++++++++++++++--
 src/test/scripts/manual/blixem/test2 | 19 +++++++++++++++++--
 src/test/scripts/manual/dotter/test1 | 19 +++++++++++++++++--
 src/test/scripts/manual/dotter/test2 | 19 +++++++++++++++++--
 src/test/scripts/manual/dotter/test3 | 19 +++++++++++++++++--
 src/test/scripts/manual/dotter/test4 | 19 +++++++++++++++++--
 src/test/scripts/manual/dotter/test5 | 19 +++++++++++++++++--
 src/test/scripts/manual/dotter/test6 | 19 +++++++++++++++++--
 src/test/scripts/manual/dotter/test7 | 19 +++++++++++++++++--
 src/test/scripts/manual/dotter/test8 | 19 +++++++++++++++++--
 15 files changed, 260 insertions(+), 30 deletions(-)

2012-04-04  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem tests no longer require pfetch to run
 src/test/data/chr4_dna_align.gff     | 1832 ++++-----
 src/test/data/chr4_protein_align.gff | 7102 +++++++++++++++++-----------------
 src/test/scripts/manual/blixem/test1 |    2 +-
 src/test/scripts/manual/blixem/test2 |    2 +-
 4 files changed, 4469 insertions(+), 4469 deletions(-)

2012-04-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a regression where matches were misaligned due to problems reading the cigar string
 src/seqtoolsUtils/blxGff3Parser.c | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

2012-03-16  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 12 ++++++++++++
 1 file changed, 12 insertions(+)

2012-03-05  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/cigar' into develop
2012-03-05  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug introduced where negative strand was not being parsed correctly
 src/seqtoolsUtils/blxGff3Parser.c | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

2012-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 Scroll-to-selection now works when matches are squashed
 src/blixemApp/detailviewtree.c | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

2012-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with sorting short read
 src/blixemApp/detailview.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 Scroll to keep selected match in view when jumping to start/end boundaries
 src/blixemApp/detailview.c | 1 +
 1 file changed, 1 insertion(+)

2012-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 Comments
 src/seqtoolsUtils/blxGff3Parser.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

2012-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with reading in gaps for reverse strand reads
 src/seqtoolsUtils/blxGff3Parser.c | 4 ++--
 src/seqtoolsUtils/blxmsp.c        | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

2012-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 Count reads as duplicates even if from different sources
 src/blixemApp/detailviewtree.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

2012-03-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug in reading bam data (wrong sequence was being used)
 src/blixemApp/blxFetch.c          |  2 +-
 src/seqtoolsUtils/blxGff3Parser.c | 12 +++++++-----
 src/seqtoolsUtils/blxmsp.c        |  7 +++++--
 3 files changed, 13 insertions(+), 8 deletions(-)

2012-03-01  Gemma Barson  <gb10@sanger.ac.uk>
 Big speed improvement when reading in large GFF files
 src/blixemApp/detailview.c    |   6 +--
 src/seqtoolsUtils/blxmsp.c    | 108 ++++++++++++++++++++++++------------------
 src/seqtoolsUtils/utilities.c |   6 ++-
 3 files changed, 69 insertions(+), 51 deletions(-)

2012-02-29  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: improvements to cigar string handling
 src/blixemApp/blixem_.h           |   2 +-
 src/blixemApp/blxFetch.c          |  26 ++++-----
 src/blixemApp/blxview.c           |   5 +-
 src/blixemApp/blxwindow.c         |  19 ++++++-
 src/blixemApp/detailview.c        |   2 +-
 src/blixemApp/detailviewtree.c    |   6 +--
 src/dotterApp/dotterMain.c        |   2 +-
 src/seqtoolsUtils/blxGff3Parser.c |  57 +++++++++++++++++---
 src/seqtoolsUtils/blxmsp.c        | 108 +++++++++++++++++++++++++++++---------
 src/seqtoolsUtils/blxmsp.h        |   3 +-
 10 files changed, 177 insertions(+), 53 deletions(-)

2012-02-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a refresh problem when selecting variations
 src/blixemApp/blxwindow.c      |  3 +--
 src/blixemApp/detailview.c     | 15 +++++++++------
 src/blixemApp/detailview.h     |  2 +-
 src/blixemApp/detailviewtree.c |  3 +--
 4 files changed, 12 insertions(+), 11 deletions(-)

2012-02-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug in protein blixem where you could not select a feature in the variations track
 src/blixemApp/detailview.c | 1379 ++++++++++++++++++++++++--------------------
 src/blixemApp/detailview.h |    5 +-
 2 files changed, 749 insertions(+), 635 deletions(-)

2012-02-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a typo on the Settings dialog (RT:254611)
 src/blixemApp/blxwindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2012-02-14  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

2012-02-10  Gemma Barson  <gb10@sanger.ac.uk>
 Updated installation instructions with better info for installing GTK on Mac
 src/INSTALL | 87 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 src/README  | 60 +++---------------------------------------
 2 files changed, 90 insertions(+), 57 deletions(-)

2012-02-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash in Belvu when running in command-line mode
 src/belvuApp/belvuAlignment.c | 6 ++++++
 1 file changed, 6 insertions(+)

2012-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some of the saved dotplots in the tests, which had the wrong zoom
 src/test/data/chr4_vs_DA730641.dot | Bin 457589 -> 455204 bytes
 src/test/data/chr4_vs_chr4.dot     | Bin 503605 -> 499366 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2012-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue in dotter where the plot outline did not coincide with the plot extents
 src/dotterApp/dotplot.c | 25 ++++++-------------------
 src/dotterApp/dotter_.h |  2 --
 2 files changed, 6 insertions(+), 21 deletions(-)

2012-02-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed bug where dotter blacks out/crashes for very long, thin plots
 src/belvuApp/belvuTree.c      |   6 --
 src/dotterApp/dotplot.c       | 154 +++++++++++++++++++++++++++++-------------
 src/dotterApp/dotter.c        |   4 +-
 src/dotterApp/dotter_.h       |   4 +-
 src/dotterApp/greyramptool.c  |  14 ----
 src/seqtoolsUtils/utilities.c |  12 ++++
 src/seqtoolsUtils/utilities.h |   1 +
 7 files changed, 125 insertions(+), 70 deletions(-)

2012-01-31  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.9' into develop
2012-01-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash during dotter shutdown
 src/dotterApp/alignmenttool.c | 7 -------
 src/dotterApp/dotter.c        | 2 --
 2 files changed, 9 deletions(-)

2012-01-25  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.9' into develop
2012-01-25  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

2012-01-25  Gemma Barson  <gb10@sanger.ac.uk>
 Display settings are now saved when exiting Blixem
 src/blixemApp/blixem_.h                  |  18 +++-
 src/blixemApp/blxwindow.c                | 175 +++++++++++++++++++++++++------
 src/blixemApp/detailview.c               |  25 ++++-
 src/blixemApp/detailview.h               |   2 +-
 src/doc/User_doc/blixem_quick_start.html |   8 +-
 5 files changed, 188 insertions(+), 40 deletions(-)

2012-01-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where exons were not always being shown in Dotter when called from blixem
 src/seqtoolsUtils/utilities.c | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

2012-01-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression where blixem was crashing after getting bam data (RT249221)
 src/seqtoolsUtils/blxGff3Parser.c | 1 -
 1 file changed, 1 deletion(-)

2012-01-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug in blixem where dotter would fail to start after opening the help page
 src/belvuApp/belvuWindow.c    |  6 ++++--
 src/blixemApp/blxdotter.c     |  7 ++++---
 src/blixemApp/blxwindow.c     |  6 ++++--
 src/dotterApp/dotter.c        |  6 ++++--
 src/seqtoolsUtils/utilities.c | 32 --------------------------------
 src/seqtoolsUtils/utilities.h |  4 ++--
 6 files changed, 18 insertions(+), 43 deletions(-)

2012-01-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression: invalid free
 src/belvuApp/belvuTree.c | 6 ------
 1 file changed, 6 deletions(-)

2012-01-17  Gemma Barson  <gb10@sanger.ac.uk>
 Updated test plan
 src/test/test_plan.ods | Bin 36754 -> 38241 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2012-01-16  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/leaks' into develop
2012-01-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some memory leaks in Belvu
 src/belvuApp/belvuTree.c | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

2012-01-16  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/leaks' into develop
2012-01-16  Gemma Barson  <gb10@sanger.ac.uk>
 More blixem leak fixes
 src/blixemApp/blixem_.h  |  4 ++--
 src/blixemApp/blxFetch.c | 19 +++++++++++--------
 src/blixemApp/blxview.c  |  2 +-
 3 files changed, 14 insertions(+), 11 deletions(-)

2012-01-16  Gemma Barson  <gb10@sanger.ac.uk>
 More blixem leak fixes
 src/blixemApp/blxFetch.c      |  2 +-
 src/blixemApp/blxmain.c       |  6 +++-
 src/blixemApp/blxview.c       |  5 +++-
 src/blixemApp/blxwindow.c     | 69 ++++++++++++++++++++++++-------------------
 src/seqtoolsUtils/blxparser.c |  4 +++
 src/seqtoolsUtils/utilities.c |  1 +
 6 files changed, 54 insertions(+), 33 deletions(-)

2012-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 More blixem leak fixes
 src/blixemApp/bigpicture.c     |  5 ++++-
 src/blixemApp/blxwindow.c      | 20 ++++++++++++++----
 src/blixemApp/detailview.c     | 22 ++++++++++++++++++--
 src/blixemApp/detailviewtree.c | 46 ++++++++++++++++++++++++++++++++++++++++--
 src/seqtoolsUtils/utilities.c  | 15 +++++++++++---
 5 files changed, 96 insertions(+), 12 deletions(-)

2012-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some leaks in blixem
 src/blixemApp/detailview.c           | 5 ++++-
 src/blixemApp/detailviewtree.c       | 9 +++++----
 src/blixemApp/sequencecellrenderer.c | 7 +++++++
 3 files changed, 16 insertions(+), 5 deletions(-)

2012-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/leaks' into develop
2012-01-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a serious leak in dotter where it was leaking every time the alignment view was scrolled
 src/seqtoolsUtils/utilities.c | 19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

2012-01-11  Gemma Barson  <gb10@sanger.ac.uk>
 More memory leak fixes
 src/dotterApp/alignmenttool.c |  6 ++++++
 src/dotterApp/dotterMain.c    | 11 ++++++++++-
 src/seqtoolsUtils/blxmsp.c    |  9 +++++++++
 3 files changed, 25 insertions(+), 1 deletion(-)

2012-01-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some memory leaks in dotter
 src/blixemApp/blixem_.h           |   2 -
 src/blixemApp/blxview.c           |  41 ------------
 src/blixemApp/blxwindow.c         |   8 ++-
 src/dotterApp/alignmenttool.c     |   9 +--
 src/dotterApp/dotplot.c           |  12 +++-
 src/dotterApp/dotter.c            | 137 +++++++++++++++++++++++++-------------
 src/dotterApp/dotterMain.c        |   7 +-
 src/dotterApp/greyramptool.c      |   7 +-
 src/seqtoolsUtils/blxGff3Parser.c |  29 ++++++--
 src/seqtoolsUtils/blxmsp.c        |  47 ++++++++++++-
 src/seqtoolsUtils/blxmsp.h        |   2 +
 src/seqtoolsUtils/utilities.c     |   5 +-
 12 files changed, 199 insertions(+), 107 deletions(-)

2012-01-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed another crash if there is no config file
 src/blixemApp/blxFetch.c | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

2012-01-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where blixem would crash if no config file is given
 src/blixemApp/blixem_.h  |  2 +-
 src/blixemApp/blxFetch.c | 12 ++++--------
 src/blixemApp/blxmain.c  |  4 +++-
 src/blixemApp/blxview.c  | 17 ++++++++---------
 4 files changed, 16 insertions(+), 19 deletions(-)

2012-01-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a buffer overrun bug introduced in commit a2b8b00
 src/blixemApp/blxFetch.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-12-07  Gemma Barson  <gb10@sanger.ac.uk>
 Updated manuals to make export to Word easier
 src/doc/User_doc/Belvu_manual.odt  | Bin 969851 -> 970098 bytes
 src/doc/User_doc/Belvu_manual.pdf  | Bin 855028 -> 819755 bytes
 src/doc/User_doc/Blixem_manual.odt | Bin 1146576 -> 994719 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 821549 -> 766962 bytes
 src/doc/User_doc/Dotter_manual.odt | Bin 463604 -> 463997 bytes
 src/doc/User_doc/Dotter_manual.pdf | Bin 342006 -> 342875 bytes
 6 files changed, 0 insertions(+), 0 deletions(-)

2011-12-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where blixem would exit if the config file did not contain pfetch groups
 src/blixemApp/blxFetch.c | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

2011-12-05  Gemma Barson  <gb10@sanger.ac.uk>
 Updated blixem manual for changes between v4.2 and v4.7
 src/doc/User_doc/Blixem_manual.odt | Bin 1102821 -> 1146576 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 855666 -> 821549 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-12-05  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed typo in configure.ac script
 src/configure.ac | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-12-02  Gemma Barson  <gb10@sanger.ac.uk>
 Updated dotter user manual for changes between v4.2 and v4.7
 src/doc/User_doc/Dotter_manual.odt | Bin 434335 -> 463604 bytes
 src/doc/User_doc/Dotter_manual.pdf | Bin 378981 -> 342006 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-12-02  Gemma Barson  <gb10@sanger.ac.uk>
 Installation scripts now exclude blixemh if libcurl not available
 src/Makefile.am  | 15 +++++++++++----
 src/README       | 40 ++++++++++++++++++----------------------
 src/configure.ac | 22 ++++++++++++++++++++--
 3 files changed, 49 insertions(+), 28 deletions(-)

2011-11-11  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2011-11-11  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.6' into production
2011-11-11  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.6' into develop
2011-11-11  Gemma Barson  <gb10@sanger.ac.uk>
 Updated version number in release notes
 src/doc/User_doc/release_notes.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-11-09  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 1 +
 1 file changed, 1 insertion(+)

2011-11-09  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/settings' into develop
2011-11-07  Gemma Barson  <gb10@sanger.ac.uk>
 Added 'reset to defaults' option on settings dialog
 src/blixemApp/blxwindow.c     | 29 +++++++++++++++++++---
 src/blixemApp/detailview.c    | 56 +++++++++++++++++++++++++++++++++++++------
 src/blixemApp/detailview.h    |  1 +
 src/seqtoolsUtils/utilities.h |  3 ++-
 4 files changed, 78 insertions(+), 11 deletions(-)

2011-11-07  Gemma Barson  <gb10@sanger.ac.uk>
 Column width settings are now saved on exit
 src/blixemApp/blixem_.h    |  4 ++++
 src/blixemApp/blxFetch.c   | 58 +++++++++++++++++++++++++++++++++++++++++-----
 src/blixemApp/blxwindow.c  | 27 +++++++++++++++++++++
 src/blixemApp/detailview.c | 29 ++++++++++++++++++++++-
 src/blixemApp/detailview.h |  1 +
 5 files changed, 112 insertions(+), 7 deletions(-)

2011-11-07  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/dynamic-loading' into develop
2011-11-07  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where CDS and UTR sections were not being shown in the detail view
 src/blixemApp/blxwindow.c | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

2011-11-07  Gemma Barson  <gb10@sanger.ac.uk>
 Small improvements to menu text
 src/blixemApp/blxwindow.c | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

2011-11-07  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a couple of bugs with dynamic loading
 src/blixemApp/blxview.c   | 9 +++++++++
 src/blixemApp/blxwindow.c | 5 +++--
 2 files changed, 12 insertions(+), 2 deletions(-)

2011-11-04  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: blixem can now dynamically load additional features on user request
 src/blixemApp/blixem_.h        |  3 +++
 src/blixemApp/blxview.c        | 47 ++++++++++++++-------------------
 src/blixemApp/blxwindow.c      | 59 +++++++++++++++++++++++++++++++++++++++++-
 src/blixemApp/detailview.c     | 13 ++++++----
 src/blixemApp/detailview.h     |  2 +-
 src/blixemApp/detailviewtree.c | 20 ++++++++++----
 src/seqtoolsUtils/blxmsp.c     | 10 +++++++
 7 files changed, 114 insertions(+), 40 deletions(-)

2011-11-03  Gemma Barson  <gb10@sanger.ac.uk>
 GdkDrawable objects are now re-used wherever possible; they were frequently being deleted and re-created before
 src/seqtoolsUtils/utilities.c | 88 ++++++++++++++++++++++++++++++++++++-------
 1 file changed, 74 insertions(+), 14 deletions(-)

2011-11-01  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

2011-10-31  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/partial-codons' into develop
2011-04-15  Gemma Barson  <gb10@sanger.ac.uk>
 Added comments
 src/seqtoolsUtils/utilities.c | 9 +++++++++
 1 file changed, 9 insertions(+)

2011-04-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed more bugs with the reading frame calculations
 src/blixemApp/bigpicture.c           |  8 ++++----
 src/blixemApp/blixem_.h              |  3 ---
 src/blixemApp/blxdotter.c            | 10 +++++-----
 src/blixemApp/blxview.c              | 13 -------------
 src/blixemApp/blxwindow.c            | 13 ++++++-------
 src/blixemApp/detailview.c           | 10 +++++-----
 src/blixemApp/detailviewtree.c       |  4 ++--
 src/blixemApp/sequencecellrenderer.c |  6 +++---
 src/seqtoolsUtils/utilities.c        |  6 +-----
 9 files changed, 26 insertions(+), 47 deletions(-)

2011-04-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression where the reference sequence reading frame was wrong
 src/blixemApp/blxwindow.c | 61 +++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 51 insertions(+), 10 deletions(-)

2011-04-15  Gemma Barson  <gb10@sanger.ac.uk>
 Partial codon boundary lines are now dotted rather than solid
 src/blixemApp/detailview.c           |  4 +-
 src/blixemApp/detailview.h           |  6 +--
 src/blixemApp/sequencecellrenderer.c | 74 +++++++++++++++++++++++++-----------
 3 files changed, 57 insertions(+), 27 deletions(-)

2011-04-15  Gemma Barson  <gb10@sanger.ac.uk>
 Made partial codon highlighting cross-hatched. Fixed a bug with rev strand coords
 src/blixemApp/bigpicture.c           |  2 +-
 src/blixemApp/blxdotter.c            |  4 ++--
 src/blixemApp/sequencecellrenderer.c | 25 ++++++++++++++++----
 src/seqtoolsUtils/utilities.c        | 46 +++---------------------------------
 4 files changed, 26 insertions(+), 51 deletions(-)

2011-04-14  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: highlight partial codons in exons
 src/blixemApp/bigpicture.c           |  6 +--
 src/blixemApp/blixem_.h              |  7 +++-
 src/blixemApp/blxdotter.c            | 10 ++---
 src/blixemApp/blxview.c              | 12 ++++++
 src/blixemApp/blxwindow.c            |  3 +-
 src/blixemApp/detailview.c           | 10 ++---
 src/blixemApp/detailviewtree.c       |  4 +-
 src/blixemApp/sequencecellrenderer.c | 55 +++++++++++++++++++++++++--
 src/seqtoolsUtils/utilities.c        | 73 ++++++++++++++++++++----------------
 9 files changed, 126 insertions(+), 54 deletions(-)

2011-10-31  Gemma Barson  <gb10@sanger.ac.uk>
 Removed unused file
 src/belvuApp/belvuOld.c | 8386 -----------------------------------------------
 1 file changed, 8386 deletions(-)

2011-10-31  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/variations' into develop
2011-10-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where selecting a SNP would select any others at the same coordinate
 src/blixemApp/detailview.c | 31 +++++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

2011-10-28  Gemma Barson  <gb10@sanger.ac.uk>
 Invert row order for variations track
 src/blixemApp/detailview.c | 113 +++++++++++++++++++++++++++++++++++++--------
 1 file changed, 95 insertions(+), 18 deletions(-)

2011-10-27  Gemma Barson  <gb10@sanger.ac.uk>
 In blixem, overlapping variations are now separated onto different rows in the variations track
 src/blixemApp/detailview.c | 66 ++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 61 insertions(+), 5 deletions(-)

2011-10-27  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/bigpicture' into develop
2011-10-26  Gemma Barson  <gb10@sanger.ac.uk>
 Horizontal mouse-wheel scrolling now works in Blixem's exon view
 src/blixemApp/exonview.c | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

2011-10-26  Gemma Barson  <gb10@sanger.ac.uk>
 Small change to remove unused code
 src/blixemApp/bigpicturegrid.c | 6 ------
 1 file changed, 6 deletions(-)

2011-10-26  Gemma Barson  <gb10@sanger.ac.uk>
 Change cursor when dragging highlight box in big picture
 src/blixemApp/bigpicture.c | 9 +++++++++
 1 file changed, 9 insertions(+)

2011-10-26  Gemma Barson  <gb10@sanger.ac.uk>
 Double-clicking in Blixem's big picture now makes the detail-view region jump (the same as middle-clicking)
 src/blixemApp/bigpicturegrid.c | 20 ++++++++++++++------
 src/blixemApp/coverageview.c   |  8 +++++---
 src/blixemApp/exonview.c       |  6 ++++--
 3 files changed, 23 insertions(+), 11 deletions(-)

2011-10-25  Gemma Barson  <gb10@sanger.ac.uk>
 Added ability to drag the highlight box in Blixem's big picture using the left mouse button
 src/blixemApp/bigpicture.c     | 57 ++++++++++++++++++++++++------------------
 src/blixemApp/bigpicture.h     |  9 ++++---
 src/blixemApp/bigpicturegrid.c | 47 +++++++++++++++++++++++-----------
 src/blixemApp/coverageview.c   | 20 +++++++++++----
 src/blixemApp/exonview.c       | 34 +++++++++++++++++--------
 src/seqtoolsUtils/utilities.c  | 11 ++++++++
 src/seqtoolsUtils/utilities.h  |  2 ++
 7 files changed, 121 insertions(+), 59 deletions(-)

2011-10-25  Gemma Barson  <gb10@sanger.ac.uk>
 Added some more dotter tests
 src/test/data/chr4_ref_seq_short.fasta             |  95 +++++++++++++++++++++
 src/test/data/chr4_vs_DA730641.dot                 | Bin 0 -> 457589 bytes
 src/test/data/chr4_vs_chr4.dot                     | Bin 0 -> 503605 bytes
 src/test/scripts/automated/dotter/test1            |   9 ++
 src/test/scripts/automated/dotter/test1_result.dot | Bin 0 -> 460197 bytes
 src/test/scripts/automated/dotter/test2            |   9 ++
 src/test/scripts/automated/dotter/test2_result.pdf | Bin 0 -> 21057 bytes
 src/test/scripts/automated/dotter/test3            |  10 +++
 src/test/scripts/automated/dotter/test3_result.dot | Bin 0 -> 460197 bytes
 src/test/scripts/automated/dotter/test3_result.pdf | Bin 0 -> 21057 bytes
 src/test/scripts/manual/dotter/test1               |   2 +-
 src/test/scripts/manual/dotter/test7               |  11 +++
 src/test/scripts/manual/dotter/test8               |  13 +++
 13 files changed, 148 insertions(+), 1 deletion(-)

2011-10-25  Gemma Barson  <gb10@sanger.ac.uk>
 Updated dotter usage
 src/doc/User_doc/dotter_usage.txt | 92 +++++++++++++++++++++++++++-----------
 src/dotterApp/dotterMain.c        | 94 ++++++++++++++++++++++++++++-----------
 2 files changed, 134 insertions(+), 52 deletions(-)

2011-10-25  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'printing' into develop
2011-10-24  Gemma Barson  <gb10@sanger.ac.uk>
 Print messages to indicate that batch mode saved/exported the plot successfully
 src/dotterApp/dotplot.c       |  2 ++
 src/dotterApp/dotterMain.c    | 17 +++++++++--------
 src/seqtoolsUtils/utilities.c |  1 +
 3 files changed, 12 insertions(+), 8 deletions(-)

2011-10-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with exporting both the dot-matrix and PDF
 src/dotterApp/dotplot.c | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

2011-10-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue with labels not being drawn on exported plots
 src/dotterApp/dotplot.c          | 70 ++++++++++++++++++++++++++++++----------
 src/dotterApp/seqtoolsExonView.c |  4 +--
 2 files changed, 55 insertions(+), 19 deletions(-)

2011-10-21  Gemma Barson  <gb10@sanger.ac.uk>
 Generalise print function
 src/belvuApp/belvuWindow.c    |   2 +-
 src/blixemApp/blxwindow.c     |   2 +-
 src/dotterApp/alignmenttool.c |   2 +-
 src/dotterApp/dotplot.c       |   2 +-
 src/dotterApp/dotter.c        |   6 +-
 src/seqtoolsUtils/utilities.c | 808 +++++++++++++++++++++---------------------
 src/seqtoolsUtils/utilities.h |   2 +-
 7 files changed, 414 insertions(+), 410 deletions(-)

2011-10-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added ability to export to PDF in dotter
 src/belvuApp/belvuWindow.c    |    2 +-
 src/blixemApp/blxwindow.c     |    2 +-
 src/dotterApp/alignmenttool.c |    2 +-
 src/dotterApp/dotplot.c       |   80 +-
 src/dotterApp/dotter.c        |  144 ++--
 src/dotterApp/dotter.h        |   13 +-
 src/dotterApp/dotterMain.c    |  776 ++++++++---------
 src/dotterApp/dotterWindow    | 1827 +++++++++++++++++++++++++++++++++++++++++
 src/dotterApp/dotter_.h       |    4 +
 src/seqtoolsUtils/utilities.c |   15 +-
 src/seqtoolsUtils/utilities.h |    2 +-
 11 files changed, 2419 insertions(+), 448 deletions(-)

2011-10-18  Gemma Barson  <gb10@sanger.ac.uk>
 Printing in dotter now prints the whole plot rather than just the scrolled window contents
 src/dotterApp/dotplot.c | 10 ++--------
 src/dotterApp/dotter.c  |  7 ++++++-
 2 files changed, 8 insertions(+), 9 deletions(-)

2011-10-18  Gemma Barson  <gb10@sanger.ac.uk>
 Updated to-do notes
 src/doc/User_doc/todo.html | 4 ----
 1 file changed, 4 deletions(-)

2011-10-17  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 1 +
 1 file changed, 1 insertion(+)

2011-10-14  Gemma Barson  <gb10@sanger.ac.uk>
 Sort by id, name and then position by default
 src/blixemApp/detailview.c | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

2011-10-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with sorting the exon view when variations and polyA features are present
 src/blixemApp/detailview.c | 27 ++++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

2011-10-13  Gemma Barson  <gb10@sanger.ac.uk>
 Exons can now be selected by clicking them in the big picture in Blixem
 src/blixemApp/exonview.c | 430 ++++++++++++++++++++++++++++++-----------------
 1 file changed, 280 insertions(+), 150 deletions(-)

2011-10-13  Gemma Barson  <gb10@sanger.ac.uk>
 Exons in Blixem's big picture are now sorted in the same order as the detail view
 src/blixemApp/blixem_.h        |   1 +
 src/blixemApp/blxview.c        |   5 +
 src/blixemApp/blxwindow.c      |   8 +-
 src/blixemApp/detailview.c     | 314 ++++++++++++++++++++++++++++++++++++++++-
 src/blixemApp/detailview.h     |   6 +
 src/blixemApp/detailviewtree.c | 248 +-------------------------------
 6 files changed, 329 insertions(+), 253 deletions(-)

2011-10-12  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 13 +++++++++++++
 1 file changed, 13 insertions(+)

2011-10-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the bumped exon view height when zooming in Dotter
 src/dotterApp/seqtoolsExonView.c | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

2011-10-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where re-draw was messed up for the dotter exon view
 src/dotterApp/seqtoolsExonView.c | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

2011-10-11  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with bumping exons for the vertical sequence in dotter
 src/dotterApp/seqtoolsExonView.c | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

2011-10-07  Gemma Barson  <gb10@sanger.ac.uk>
 Added the ability to bump exons in dotter
 src/dotterApp/dotplot.c          |  8 ++++++++
 src/dotterApp/dotter.c           | 12 +++++++++++-
 src/dotterApp/dotter_.h          |  1 +
 src/dotterApp/seqtoolsExonView.c | 13 ++++++++-----
 src/dotterApp/seqtoolsExonView.h |  2 +-
 5 files changed, 29 insertions(+), 7 deletions(-)

2011-10-06  Gemma Barson  <gb10@sanger.ac.uk>
 Shade the border in dotter where the matrix cannot be calculated
 src/dotterApp/dotplot.c | 20 +++++++++++++++++++-
 src/dotterApp/dotter.c  |  1 +
 src/dotterApp/dotter_.h |  1 +
 3 files changed, 21 insertions(+), 1 deletion(-)

2011-10-05  Gemma Barson  <gb10@sanger.ac.uk>
 RT95637: made blixem window title more informative
 src/blixemApp/blxview.c | 59 ++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 53 insertions(+), 6 deletions(-)

2011-10-03  Gemma Barson  <gb10@sanger.ac.uk>
 Small change to test scripts - pass annotation arg for blixem tests
 src/test/scripts/manual/blixem/test1 | 2 +-
 src/test/scripts/manual/blixem/test2 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

2011-10-03  Gemma Barson  <gb10@sanger.ac.uk>
 Added belvu manual to help page and distribution
 src/Makefile.am                         | 4 ++--
 src/doc/User_doc/belvu_quick_start.html | 2 +-
 src/doc/User_doc/manuals.html           | 2 ++
 3 files changed, 5 insertions(+), 3 deletions(-)

2011-10-03  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes for version 4.5
 src/doc/User_doc/release_notes.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-09-30  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'production' into develop
2011-09-30  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.5' into production
2011-09-30  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'release/4.5' into develop
2011-09-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the pfetch window size in pfetch-http mode
 src/seqtoolsUtils/utilities.c | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

2011-09-28  Gemma Barson  <gb10@sanger.ac.uk>
 Comments and formatting
 src/belvuApp/belvuAlignment.c | 68 +++++++++++++++++++++++++------------------
 src/belvuApp/belvuMain.c      | 23 +++------------
 2 files changed, 44 insertions(+), 47 deletions(-)

2011-09-28  Gemma Barson  <gb10@sanger.ac.uk>
 Small update to belvu manual
 src/doc/User_doc/Belvu_manual.odt | Bin 969893 -> 969851 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2011-09-28  Gemma Barson  <gb10@sanger.ac.uk>
 Added first draft of design notes for belvu
 src/doc/Design_notes/architecture.html      |  1 +
 src/doc/Design_notes/modules/belvuApp.html  | 88 +++++++++++++++++++++++++++++
 src/doc/Design_notes/modules/dotterApp.html |  2 +-
 3 files changed, 90 insertions(+), 1 deletion(-)

2011-09-23  Gemma Barson  <gb10@sanger.ac.uk>
 Improved code comments
 src/belvuApp/belvu.c  | 116 +++++++++++++++++++++++++++++++++++---------------
 src/belvuApp/belvu_.h |   2 +-
 2 files changed, 82 insertions(+), 36 deletions(-)

2011-09-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where belvu could index out of the end of the string for short markup lines
 src/belvuApp/belvuAlignment.c | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

2011-09-22  Gemma Barson  <gb10@sanger.ac.uk>
 Added extended usage info
 src/belvuApp/belvuMain.c         | 202 ++++++++++++++++++++++++++++++++++++---
 src/doc/User_doc/belvu_usage.txt | 127 ++++++++++++++++++++----
 2 files changed, 302 insertions(+), 27 deletions(-)

2011-09-22  Gemma Barson  <gb10@sanger.ac.uk>
 Added Belvu user manual
 src/doc/User_doc/Belvu_manual.odt | Bin 0 -> 969893 bytes
 src/doc/User_doc/Belvu_manual.pdf | Bin 0 -> 855028 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 Moved dotter tests to own directory
 src/test/scripts/manual/{blixem/test3 => dotter/test1} | 0
 src/test/scripts/manual/{blixem/test4 => dotter/test2} | 0
 src/test/scripts/manual/{blixem/test5 => dotter/test3} | 0
 src/test/scripts/manual/{blixem/test6 => dotter/test4} | 0
 src/test/scripts/manual/{blixem/test7 => dotter/test5} | 0
 src/test/scripts/manual/{blixem/test8 => dotter/test6} | 0
 6 files changed, 0 insertions(+), 0 deletions(-)

2011-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/testing' into develop
2011-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 More dotter tests
 src/test/data/chr4_translation_frame1.fasta |  5 +++++
 src/test/scripts/manual/blixem/test6        |  4 ++--
 src/test/scripts/manual/blixem/test7        | 13 +++++++++++++
 src/test/scripts/manual/blixem/test8        | 10 ++++++++++
 4 files changed, 30 insertions(+), 2 deletions(-)

2011-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 Updated test comments
 src/test/scripts/manual/blixem/test3 |  3 ++-
 src/test/scripts/manual/blixem/test5 |  3 ++-
 src/test/scripts/manual/blixem/test6 |  8 ++++----
 src/test/scripts/manual/blixem/test7 | 12 ------------
 4 files changed, 8 insertions(+), 18 deletions(-)

2011-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added more dotter tests
 src/test/scripts/manual/blixem/test5 |  2 +-
 src/test/scripts/manual/blixem/test6 | 12 ++++++++++++
 src/test/scripts/manual/blixem/test7 | 12 ++++++++++++
 3 files changed, 25 insertions(+), 1 deletion(-)

2011-09-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added another dotter test
 src/test/data/Q9H8G1.fasta           | 11 +++++++++++
 src/test/scripts/manual/blixem/test5 |  4 ++--
 2 files changed, 13 insertions(+), 2 deletions(-)

2011-09-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added blixem and dotter tests
 src/test/data/DA730641.fasta                     | 16 ++++++++++++++++
 src/test/data/{chr4.fasta => chr4_ref_seq.fasta} |  0
 src/test/scripts/manual/blixem/test1             | 11 ++++++++++-
 src/test/scripts/manual/blixem/test2             | 11 ++++++++++-
 src/test/scripts/manual/blixem/test3             | 14 ++++++++++++++
 src/test/scripts/manual/blixem/test4             | 15 +++++++++++++++
 src/test/scripts/manual/blixem/test5             | 14 ++++++++++++++
 7 files changed, 79 insertions(+), 2 deletions(-)

2011-09-14  Gemma Barson  <gb10@sanger.ac.uk>
 Removed executables from gitignore
 .gitignore | 6 ------
 1 file changed, 6 deletions(-)

2011-09-14  Gemma Barson  <gb10@sanger.ac.uk>
 Added blixem tests
 src/test/data/chr4.fasta             | 2256 ++++++++++++++++
 src/test/data/chr4_dna_align.gff     | 2269 ++++++++++++++++
 src/test/data/chr4_protein_align.gff | 4904 ++++++++++++++++++++++++++++++++++
 src/test/scripts/manual/blixem/test1 |    2 +
 src/test/scripts/manual/blixem/test2 |    2 +
 5 files changed, 9433 insertions(+)

2011-09-12  Gemma Barson  <gb10@sanger.ac.uk>
 Moved tests to toplevel test directory
 src/Makefile.am                                             |   5 +++--
 src/doc/Design_notes/specs.html                             |   2 +-
 src/doc/Design_notes/tests/README                           |  10 ----------
 src/test/README                                             |  12 ++++++++++++
 src/{doc/Design_notes/tests => test}/data/ALIGN.fasta       |   0
 src/{doc/Design_notes/tests => test}/data/ALIGN.selex       |   0
 .../Design_notes/tests => test}/data/PF02171_full.selex     |   0
 .../Design_notes/tests => test}/data/PF02171_full.stock     |   0
 .../Design_notes/tests => test}/data/PF02171_seed.fasta     |   0
 src/{doc/Design_notes/tests => test}/data/PF02171_seed.msf  |   0
 .../Design_notes/tests => test}/data/PF02171_seed.scores    |   0
 src/{doc/Design_notes/tests => test}/data/PF02171_seed.segs |   0
 .../Design_notes/tests => test}/data/PF02171_seed.selex     |   0
 .../Design_notes/tests => test}/data/PF02171_seed.stock     |   0
 .../tests => test}/data/PF02171_seed_segs.stock             |   0
 .../tests => test}/data/PF02171_seed_separator.stock        |   0
 src/{doc/Design_notes/tests => test}/data/cgph_pale.color   |   0
 src/{doc/Design_notes/tests => test}/data/cgph_pale2.color  |   0
 src/{doc/Design_notes/tests => test}/data/markup.color      |   0
 src/{doc/Design_notes/tests => test}/data/markup2.color     |   0
 .../Design_notes/tests => test}/data/markup_content.selex   |   0
 .../Design_notes/tests => test}/data/markup_headers.selex   |   0
 .../command_line => test/scripts/automated/belvu}/test1     |   0
 .../command_line => test/scripts/automated/belvu}/test10    |   0
 .../scripts/automated/belvu}/test10_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test11    |   0
 .../scripts/automated/belvu}/test11_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test12    |   0
 .../scripts/automated/belvu}/test12_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test13    |   0
 .../scripts/automated/belvu}/test13_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test14    |   0
 .../scripts/automated/belvu}/test14_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test15    |   0
 .../scripts/automated/belvu}/test15_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test16    |   0
 .../scripts/automated/belvu}/test16_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test17    |   0
 .../scripts/automated/belvu}/test17_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test18    |   0
 .../scripts/automated/belvu}/test18_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test19    |   0
 .../scripts/automated/belvu}/test19_results                 |   0
 .../scripts/automated/belvu}/test1_results                  |   0
 .../command_line => test/scripts/automated/belvu}/test2     |   0
 .../command_line => test/scripts/automated/belvu}/test20    |   0
 .../scripts/automated/belvu}/test20_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test21    |   0
 .../scripts/automated/belvu}/test21_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test22    |   0
 .../scripts/automated/belvu}/test22_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test23    |   0
 .../scripts/automated/belvu}/test23_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test24    |   0
 .../scripts/automated/belvu}/test24_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test25    |   0
 .../scripts/automated/belvu}/test25_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test26    |   0
 .../scripts/automated/belvu}/test26_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test27    |   0
 .../scripts/automated/belvu}/test27_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test28    |   0
 .../scripts/automated/belvu}/test28_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test29    |   0
 .../scripts/automated/belvu}/test29_results                 |   0
 .../scripts/automated/belvu}/test2_results                  |   0
 .../command_line => test/scripts/automated/belvu}/test3     |   0
 .../command_line => test/scripts/automated/belvu}/test30    |   0
 .../scripts/automated/belvu}/test30_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test31    |   0
 .../scripts/automated/belvu}/test31_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test32    |   0
 .../scripts/automated/belvu}/test32_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test33    |   0
 .../scripts/automated/belvu}/test33_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test34    |   0
 .../scripts/automated/belvu}/test34_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test35    |   0
 .../scripts/automated/belvu}/test35_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test36    |   0
 .../scripts/automated/belvu}/test36_results                 |   0
 .../scripts/automated/belvu}/test36_results_old             |   0
 .../command_line => test/scripts/automated/belvu}/test37    |   0
 .../scripts/automated/belvu}/test37_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test38    |   0
 .../scripts/automated/belvu}/test38_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test39    |   0
 .../scripts/automated/belvu}/test39_results                 |   0
 .../scripts/automated/belvu}/test3_results                  |   0
 .../command_line => test/scripts/automated/belvu}/test4     |   0
 .../command_line => test/scripts/automated/belvu}/test40    |   0
 .../scripts/automated/belvu}/test40_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test41    |   0
 .../scripts/automated/belvu}/test41_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test42    |   0
 .../scripts/automated/belvu}/test42_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test43    |   0
 .../scripts/automated/belvu}/test43_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test44    |   0
 .../scripts/automated/belvu}/test44_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test45    |   0
 .../scripts/automated/belvu}/test45_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test46    |   0
 .../scripts/automated/belvu}/test46_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test47    |   0
 .../scripts/automated/belvu}/test47_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test48    |   0
 .../scripts/automated/belvu}/test48_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test49    |   0
 .../scripts/automated/belvu}/test49_results                 |   0
 .../scripts/automated/belvu}/test4_results                  |   0
 .../command_line => test/scripts/automated/belvu}/test5     |   0
 .../command_line => test/scripts/automated/belvu}/test50    |   0
 .../scripts/automated/belvu}/test50_results                 |   0
 .../command_line => test/scripts/automated/belvu}/test51    |   0
 .../scripts/automated/belvu}/test51_results                 |   0
 .../scripts/automated/belvu}/test5_results                  |   0
 .../command_line => test/scripts/automated/belvu}/test6     |   0
 .../scripts/automated/belvu}/test6_results                  |   0
 .../command_line => test/scripts/automated/belvu}/test7     |   0
 .../scripts/automated/belvu}/test7_results                  |   0
 .../command_line => test/scripts/automated/belvu}/test8     |   0
 .../scripts/automated/belvu}/test8_results                  |   0
 .../command_line => test/scripts/automated/belvu}/test9     |   0
 .../scripts/automated/belvu}/test9_results                  |   0
 .../tests/gui => test/scripts/manual/belvu}/test1           |   0
 .../tests/gui => test/scripts/manual/belvu}/test2           |   0
 .../tests/gui => test/scripts/manual/belvu}/test3           |   0
 .../tests/gui => test/scripts/manual/belvu}/test4           |   0
 .../tests/gui => test/scripts/manual/belvu}/test5           |   0
 src/{doc/Design_notes/testing.ods => test/test_plan.ods}    | Bin
 131 files changed, 16 insertions(+), 13 deletions(-)

2011-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 Small update to dotter usage text
 src/dotterApp/dotterMain.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-09-21  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with rev-comping sequences in dotter
 src/dotterApp/dotterMain.c | 38 ++++++++++++++++++++++++++++++--------
 1 file changed, 30 insertions(+), 8 deletions(-)

2011-09-20  Gemma Barson  <gb10@sanger.ac.uk>
 Performance improvements to middle-dragging on the tree
 src/blixemApp/bigpicture.c     |  16 ++++-
 src/blixemApp/blixem_.h        |   3 +-
 src/blixemApp/blxwindow.c      |  13 +++-
 src/blixemApp/coverageview.c   |   8 ++-
 src/blixemApp/detailview.c     |  63 ++++++++++++------
 src/blixemApp/detailview.h     |   2 +-
 src/blixemApp/detailviewtree.c | 148 +++++++++++++++++++++++++++++++++++------
 src/blixemApp/detailviewtree.h |   7 +-
 src/seqtoolsUtils/utilities.c  |  24 +++++++
 src/seqtoolsUtils/utilities.h  |   1 +
 10 files changed, 237 insertions(+), 48 deletions(-)

2011-09-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a potential crash when finding sequences if feature name to match against is null
 src/blixemApp/blxwindow.c | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

2011-09-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression with gapped protein alignments
 src/blixemApp/blxmain.c | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

2011-09-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a backwards compatibility issue where blast mode was not being set correctly
 src/blixemApp/blxmain.c           | 85 ++++++++++++++++++++++-----------------
 src/seqtoolsUtils/blxGff3Parser.c | 10 ++++-
 2 files changed, 56 insertions(+), 39 deletions(-)

2011-09-09  Gemma Barson  <gb10@sanger.ac.uk>
 Better handling of bad characters in fasta files
 src/blixemApp/blixem_.h       |  2 +-
 src/blixemApp/blxmain.c       | 16 +++++-----
 src/blixemApp/blxwindow.c     |  2 +-
 src/blixemApp/detailview.c    | 10 +++----
 src/dotterApp/dotplot.c       |  4 +--
 src/seqtoolsUtils/blxparser.c | 70 ++++++++++++++++++++++++++-----------------
 src/seqtoolsUtils/utilities.c | 46 ++++++++--------------------
 src/seqtoolsUtils/utilities.h | 13 ++++----
 8 files changed, 80 insertions(+), 83 deletions(-)

2011-09-09  Gemma Barson  <gb10@sanger.ac.uk>
 Removed . and space from iupac list of valid characters, because only - is a valid gap char in fasta files
 src/seqtoolsUtils/iupac.h | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

2011-09-09  Gemma Barson  <gb10@sanger.ac.uk>
 Dotter now gives a better error message if it fails to determine the sequence type of its inputs
 src/blixemApp/blxview.c       |  6 +++++-
 src/dotterApp/dotplot.c       |  3 ---
 src/dotterApp/dotterMain.c    | 19 +++++++++++++------
 src/seqtoolsUtils/utilities.c | 19 +++++++++++++------
 src/seqtoolsUtils/utilities.h |  5 +++--
 5 files changed, 34 insertions(+), 18 deletions(-)

2011-09-09  Gemma Barson  <gb10@sanger.ac.uk>
 Improved fasta sequence validation
 src/blixemApp/blxview.c              |  6 +--
 src/blixemApp/sequencecellrenderer.c |  4 +-
 src/seqtoolsUtils/blxparser.c        |  7 ---
 src/seqtoolsUtils/iupac.h            | 25 +++++++++-
 src/seqtoolsUtils/translate.c        | 91 +++++++++++++++++-------------------
 src/seqtoolsUtils/utilities.c        | 24 +++++-----
 src/seqtoolsUtils/utilities.h        | 14 +++---
 7 files changed, 92 insertions(+), 79 deletions(-)

2011-09-08  Gemma Barson  <gb10@sanger.ac.uk>
 GFF parser now also checks fasta input for invalid characters
 src/seqtoolsUtils/blxparser.c | 8 ++++++++
 1 file changed, 8 insertions(+)

2011-09-08  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem now gives warnings if input fasta sequence contains invalid characters
 src/seqtoolsUtils/blxparser.c | 7 +++++++
 src/seqtoolsUtils/utilities.c | 4 ++--
 2 files changed, 9 insertions(+), 2 deletions(-)

2011-09-08  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-09-08  Gemma Barson  <gb10@sanger.ac.uk>
 Make sure assembly gaps are always visible, even when zoomed out
 src/blixemApp/blxview.c | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

2011-09-08  Gemma Barson  <gb10@sanger.ac.uk>
 Assembly gaps are now calculated from reference sequence
 src/blixemApp/blxview.c           | 42 +++++++++++++++++++++++++++++++++++++--
 src/seqtoolsUtils/blxGff3Parser.c |  1 -
 src/seqtoolsUtils/utilities.h     |  1 +
 3 files changed, 41 insertions(+), 3 deletions(-)

2011-09-08  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 1 +
 1 file changed, 1 insertion(+)

2011-09-08  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a major performance issue when reading files with many annotation lines
 src/belvuApp/belvu.c | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

2011-08-31  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release notes
 src/doc/User_doc/release_notes.html | 2 ++
 1 file changed, 2 insertions(+)

2011-08-31  Gemma Barson  <gb10@sanger.ac.uk>
 Ensure all error messages are terminated by a newline
 src/belvuApp/belvu.c       | 38 +++++++++++++++++++-------------------
 src/belvuApp/belvuMain.c   | 34 +++++++++++++++++-----------------
 src/belvuApp/belvuTree.c   |  4 ++--
 src/dotterApp/dotplot.c    |  2 +-
 src/dotterApp/dotter.c     | 12 ++++++------
 src/dotterApp/dotterMain.c |  6 +++---
 6 files changed, 48 insertions(+), 48 deletions(-)

2011-08-31  Gemma Barson  <gb10@sanger.ac.uk>
 Small change to pfetch window max height
 src/seqtoolsUtils/utilities.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-08-31  Gemma Barson  <gb10@sanger.ac.uk>
 Improved pfetch window size
 src/belvuApp/belvuWindow.c    |   2 +-
 src/blixemApp/blxwindow.c     |   2 +-
 src/seqtoolsUtils/utilities.c | 106 +++++++++++++++++++++++++-----------------
 src/seqtoolsUtils/utilities.h |   3 ++
 4 files changed, 69 insertions(+), 44 deletions(-)

2011-08-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the Custom menu item was not selected on startup when loading a color file
 src/belvuApp/belvuWindow.c | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

2011-08-31  Gemma Barson  <gb10@sanger.ac.uk>
 Improved installation notes on the readme file
 src/README | 46 +++++++++++++++++++++++++++++-----------------
 1 file changed, 29 insertions(+), 17 deletions(-)

2011-08-19  Gemma Barson  <gb10@sanger.ac.uk>
 Removed future release number from release notes
 src/doc/User_doc/release_notes.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-08-19  Gemma Barson  <gb10@sanger.ac.uk>
 Small change to readme file contact details
 src/README | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-08-19  Gemma Barson  <gb10@sanger.ac.uk>
 Renamed release-notes file
 src/Makefile.am                          | 2 +-
 src/NEWS                                 | 2 +-
 src/doc/User_doc/belvu_quick_start.html  | 4 ++--
 src/doc/User_doc/blixem_quick_start.html | 4 ++--
 src/doc/User_doc/dotter_quick_start.html | 4 ++--
 src/doc/User_doc/index.html              | 2 +-
 6 files changed, 9 insertions(+), 9 deletions(-)

2011-08-19  Gemma Barson  <gb10@sanger.ac.uk>
 Renamed release-notes file
 src/doc/User_doc/{news.html => release_notes.html} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

2011-08-19  Gemma Barson  <gb10@sanger.ac.uk>
 Added note about usage to readme file
 src/README | 5 +++++
 1 file changed, 5 insertions(+)

2011-08-19  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to help pages; updated what's new for next release
 src/AUTHORS                              |   6 +-
 src/Makefile.am                          |   3 +-
 src/NEWS                                 |   5 +-
 src/doc/User_doc/belvu_news.html         |  43 -------
 src/doc/User_doc/belvu_quick_start.html  |   4 +-
 src/doc/User_doc/blixem_news.html        |  86 -------------
 src/doc/User_doc/blixem_quick_start.html |   4 +-
 src/doc/User_doc/dotter_news.html        |  56 ---------
 src/doc/User_doc/dotter_quick_start.html |   4 +-
 src/doc/User_doc/index.html              |   4 +-
 src/doc/User_doc/news.html               | 203 +++++++++++++++++++++++++++++++
 src/doc/User_doc/todo.html               |  56 ++++-----
 12 files changed, 237 insertions(+), 237 deletions(-)

2011-08-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed problem with autoconf convenience libraries
 src/Makefile.am | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

2011-08-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with autoconf
 src/Makefile.am | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-08-16  Gemma Barson  <gb10@sanger.ac.uk>
 Removed obsolete version number
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-08-16  Gemma Barson  <gb10@sanger.ac.uk>
 Small update to readme file
 src/README | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2011-08-16  Gemma Barson  <gb10@sanger.ac.uk>
 Building individual targets now finds dependencies
 src/Makefile.am               | 74 +++++++++++++++++++++++++++++++++++++++----
 src/belvuApp/Makefile.am      | 12 -------
 src/blixemApp/Makefile.am     |  8 -----
 src/configure.ac              | 11 ++++---
 src/doc/Makefile.am           |  4 ---
 src/doc/User_doc/Makefile.am  | 10 ------
 src/dotterApp/Makefile.am     |  8 -----
 src/libpfetch/Makefile.am     | 29 -----------------
 src/seqtoolsUtils/Makefile.am |  8 -----
 src/seqtoolsUtils/translate.c |  2 +-
 10 files changed, 74 insertions(+), 92 deletions(-)

2011-08-16  Gemma Barson  <gb10@sanger.ac.uk>
 Updated readme with info about belvu
 src/README | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

2011-08-15  Gemma Barson  <gb10@sanger.ac.uk>
 Added in old-style ascii arrows to remove-left/remove-right menu options
 src/belvuApp/belvuWindow.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-08-12  Gemma Barson  <gb10@sanger.ac.uk>
 Small update to belvu what's-new doc
 src/doc/User_doc/belvu_news.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-08-12  Gemma Barson  <gb10@sanger.ac.uk>
 Can now set zero statusbar height to hide statusbar
 src/belvuApp/belvuMain.c         | 2 +-
 src/belvuApp/belvuWindow.c       | 8 +++++++-
 src/doc/User_doc/belvu_usage.txt | 2 +-
 3 files changed, 9 insertions(+), 3 deletions(-)

2011-08-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a broken link in the belvu help page
 src/doc/User_doc/belvu_quick_start.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-08-12  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/belvu' into develop
2011-08-12  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to alignment view padding
 src/belvuApp/belvuAlignment.c | 56 +++++--------------------------------------
 1 file changed, 6 insertions(+), 50 deletions(-)

2011-08-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the columns were not being resized correctly after deleting sequences
 src/belvuApp/belvu.c | 5 +++++
 1 file changed, 5 insertions(+)

2011-08-11  Gemma Barson  <gb10@sanger.ac.uk>
 Added belvu tests
 src/doc/Design_notes/tests/README                  |   10 +
 src/doc/Design_notes/tests/command_line/test1      |    4 +
 src/doc/Design_notes/tests/command_line/test10     |    5 +
 .../Design_notes/tests/command_line/test10_results |   45 +
 src/doc/Design_notes/tests/command_line/test11     |    5 +
 .../Design_notes/tests/command_line/test11_results | 1110 ++++++
 src/doc/Design_notes/tests/command_line/test12     |    5 +
 .../Design_notes/tests/command_line/test12_results | 2524 ++++++++++++++
 src/doc/Design_notes/tests/command_line/test13     |    5 +
 .../Design_notes/tests/command_line/test13_results |   61 +
 src/doc/Design_notes/tests/command_line/test14     |    6 +
 .../Design_notes/tests/command_line/test14_results | 2524 ++++++++++++++
 src/doc/Design_notes/tests/command_line/test15     |    5 +
 .../Design_notes/tests/command_line/test15_results |   61 +
 src/doc/Design_notes/tests/command_line/test16     |    6 +
 .../Design_notes/tests/command_line/test16_results | 2524 ++++++++++++++
 src/doc/Design_notes/tests/command_line/test17     |    6 +
 .../Design_notes/tests/command_line/test17_results | 2524 ++++++++++++++
 src/doc/Design_notes/tests/command_line/test18     |    5 +
 .../Design_notes/tests/command_line/test18_results | 2524 ++++++++++++++
 src/doc/Design_notes/tests/command_line/test19     |    4 +
 .../Design_notes/tests/command_line/test19_results |    2 +
 .../Design_notes/tests/command_line/test1_results  |  226 ++
 src/doc/Design_notes/tests/command_line/test2      |    4 +
 src/doc/Design_notes/tests/command_line/test20     |    5 +
 .../Design_notes/tests/command_line/test20_results |  380 +++
 src/doc/Design_notes/tests/command_line/test21     |    5 +
 .../Design_notes/tests/command_line/test21_results | 1119 ++++++
 src/doc/Design_notes/tests/command_line/test22     |    5 +
 .../Design_notes/tests/command_line/test22_results |   43 +
 src/doc/Design_notes/tests/command_line/test23     |    5 +
 .../Design_notes/tests/command_line/test23_results | 3544 ++++++++++++++++++++
 src/doc/Design_notes/tests/command_line/test24     |    4 +
 .../Design_notes/tests/command_line/test24_results |   48 +
 src/doc/Design_notes/tests/command_line/test25     |    5 +
 .../Design_notes/tests/command_line/test25_results |   58 +
 src/doc/Design_notes/tests/command_line/test26     |    9 +
 .../Design_notes/tests/command_line/test26_results |  226 ++
 src/doc/Design_notes/tests/command_line/test27     |    9 +
 .../Design_notes/tests/command_line/test27_results |  226 ++
 src/doc/Design_notes/tests/command_line/test28     |    5 +
 .../Design_notes/tests/command_line/test28_results |    2 +
 src/doc/Design_notes/tests/command_line/test29     |    6 +
 .../Design_notes/tests/command_line/test29_results |    2 +
 .../Design_notes/tests/command_line/test2_results  |   58 +
 src/doc/Design_notes/tests/command_line/test3      |    4 +
 src/doc/Design_notes/tests/command_line/test30     |    6 +
 .../Design_notes/tests/command_line/test30_results |    2 +
 src/doc/Design_notes/tests/command_line/test31     |    6 +
 .../Design_notes/tests/command_line/test31_results |  110 +
 src/doc/Design_notes/tests/command_line/test32     |    6 +
 .../Design_notes/tests/command_line/test32_results |  147 +
 src/doc/Design_notes/tests/command_line/test33     |    6 +
 .../Design_notes/tests/command_line/test33_results |   23 +
 src/doc/Design_notes/tests/command_line/test34     |    5 +
 .../Design_notes/tests/command_line/test34_results |   23 +
 src/doc/Design_notes/tests/command_line/test35     |    5 +
 .../Design_notes/tests/command_line/test35_results |  371 ++
 src/doc/Design_notes/tests/command_line/test36     |    5 +
 .../Design_notes/tests/command_line/test36_results |  843 +++++
 .../tests/command_line/test36_results_old          |  843 +++++
 src/doc/Design_notes/tests/command_line/test37     |    5 +
 .../Design_notes/tests/command_line/test37_results |  843 +++++
 src/doc/Design_notes/tests/command_line/test38     |    5 +
 .../Design_notes/tests/command_line/test38_results |  371 ++
 src/doc/Design_notes/tests/command_line/test39     |    5 +
 .../Design_notes/tests/command_line/test39_results |  371 ++
 .../Design_notes/tests/command_line/test3_results  |   58 +
 src/doc/Design_notes/tests/command_line/test4      |    4 +
 src/doc/Design_notes/tests/command_line/test40     |    5 +
 .../Design_notes/tests/command_line/test40_results |   24 +
 src/doc/Design_notes/tests/command_line/test41     |    5 +
 .../Design_notes/tests/command_line/test41_results | 1108 ++++++
 src/doc/Design_notes/tests/command_line/test42     |    5 +
 .../Design_notes/tests/command_line/test42_results | 1108 ++++++
 src/doc/Design_notes/tests/command_line/test43     |    5 +
 .../Design_notes/tests/command_line/test43_results | 1108 ++++++
 src/doc/Design_notes/tests/command_line/test44     |    5 +
 .../Design_notes/tests/command_line/test44_results | 1108 ++++++
 src/doc/Design_notes/tests/command_line/test45     |    5 +
 .../Design_notes/tests/command_line/test45_results | 1108 ++++++
 src/doc/Design_notes/tests/command_line/test46     |    5 +
 .../Design_notes/tests/command_line/test46_results | 1108 ++++++
 src/doc/Design_notes/tests/command_line/test47     |    5 +
 .../Design_notes/tests/command_line/test47_results | 1108 ++++++
 src/doc/Design_notes/tests/command_line/test48     |    5 +
 .../Design_notes/tests/command_line/test48_results | 1108 ++++++
 src/doc/Design_notes/tests/command_line/test49     |    5 +
 .../Design_notes/tests/command_line/test49_results | 1108 ++++++
 .../Design_notes/tests/command_line/test4_results  |  147 +
 src/doc/Design_notes/tests/command_line/test5      |    4 +
 src/doc/Design_notes/tests/command_line/test50     |    5 +
 .../Design_notes/tests/command_line/test50_results | 1108 ++++++
 src/doc/Design_notes/tests/command_line/test51     |    5 +
 .../Design_notes/tests/command_line/test51_results |   24 +
 .../Design_notes/tests/command_line/test5_results  |  110 +
 src/doc/Design_notes/tests/command_line/test6      |    4 +
 .../Design_notes/tests/command_line/test6_results  |   61 +
 src/doc/Design_notes/tests/command_line/test7      |    4 +
 .../Design_notes/tests/command_line/test7_results  |  417 +++
 src/doc/Design_notes/tests/command_line/test8      |    5 +
 .../Design_notes/tests/command_line/test8_results  | 3544 ++++++++++++++++++++
 src/doc/Design_notes/tests/command_line/test9      |    5 +
 .../Design_notes/tests/command_line/test9_results  |  236 ++
 src/doc/Design_notes/tests/data/ALIGN.fasta        |  740 ++++
 src/doc/Design_notes/tests/data/ALIGN.selex        |  370 ++
 src/doc/Design_notes/tests/data/PF02171_full.selex |  842 +++++
 src/doc/Design_notes/tests/data/PF02171_full.stock | 1739 ++++++++++
 src/doc/Design_notes/tests/data/PF02171_seed.fasta |  176 +
 src/doc/Design_notes/tests/data/PF02171_seed.msf   |  215 ++
 .../Design_notes/tests/data/PF02171_seed.scores    |   33 +
 src/doc/Design_notes/tests/data/PF02171_seed.segs  |    4 +
 src/doc/Design_notes/tests/data/PF02171_seed.selex |   45 +
 src/doc/Design_notes/tests/data/PF02171_seed.stock |   59 +
 .../tests/data/PF02171_seed_segs.stock             |   63 +
 .../tests/data/PF02171_seed_separator.stock        |   59 +
 src/doc/Design_notes/tests/data/cgph_pale.color    |   20 +
 src/doc/Design_notes/tests/data/cgph_pale2.color   |    5 +
 src/doc/Design_notes/tests/data/markup.color       |   20 +
 src/doc/Design_notes/tests/data/markup2.color      |    3 +
 .../Design_notes/tests/data/markup_content.selex   |   20 +
 .../Design_notes/tests/data/markup_headers.selex   |   32 +
 src/doc/Design_notes/tests/gui/test1               |   11 +
 src/doc/Design_notes/tests/gui/test2               |    9 +
 src/doc/Design_notes/tests/gui/test3               |    5 +
 src/doc/Design_notes/tests/gui/test4               |   10 +
 src/doc/Design_notes/tests/gui/test5               |    9 +
 127 files changed, 44240 insertions(+)

2011-08-11  Gemma Barson  <gb10@sanger.ac.uk>
 Updated belvu what's new notes
 src/doc/User_doc/belvu_news.html | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

2011-08-11  Gemma Barson  <gb10@sanger.ac.uk>
 Added notes about gtkrc to belvu quick start guide
 src/doc/User_doc/belvu_quick_start.html | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

2011-08-11  Gemma Barson  <gb10@sanger.ac.uk>
 Updated belvu usage with new environment variable
 src/doc/User_doc/belvu_usage.txt | 1 +
 1 file changed, 1 insertion(+)

2011-08-11  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed bugs with font size
 src/belvuApp/belvu.c          |  8 ++++++--
 src/belvuApp/belvuAlignment.c |  3 +--
 src/belvuApp/belvuMain.c      |  3 ++-
 src/belvuApp/belvuWindow.c    | 25 +++++++++++++------------
 src/belvuApp/belvu_.h         |  2 ++
 5 files changed, 24 insertions(+), 17 deletions(-)

2011-08-11  Gemma Barson  <gb10@sanger.ac.uk>
 Made sure all messages are terminated with a newline
 src/belvuApp/belvu.c       | 24 ++++++++++++------------
 src/belvuApp/belvuWindow.c |  4 ++--
 2 files changed, 14 insertions(+), 14 deletions(-)

2011-08-11  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the alignment width not being calculated correctly
 src/belvuApp/belvuAlignment.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-08-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with displaying more than one assembly gap
 src/blixemApp/blxview.c | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

2011-08-10  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/assembly-gaps' into develop
2011-08-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with displaying assembly gaps when display is reversed
 src/blixemApp/bigpicture.c     |  6 +++++-
 src/blixemApp/bigpicturegrid.c |  6 +++++-
 src/blixemApp/blixem_.h        |  2 +-
 src/blixemApp/blxview.c        | 10 +++++-----
 src/blixemApp/exonview.c       |  6 +++++-
 5 files changed, 21 insertions(+), 9 deletions(-)

2011-08-10  Gemma Barson  <gb10@sanger.ac.uk>
 Assembly gaps are now highlighted in the big picture
 src/blixemApp/bigpicture.c     |  5 +++++
 src/blixemApp/bigpicturegrid.c |  7 +++++++
 src/blixemApp/blixem_.h        |  9 +++++++++
 src/blixemApp/blxview.c        | 38 ++++++++++++++++++++++++++++++++++++++
 src/blixemApp/blxwindow.c      |  1 +
 src/blixemApp/exonview.c       |  7 ++++++-
 src/seqtoolsUtils/utilities.h  |  1 +
 7 files changed, 67 insertions(+), 1 deletion(-)

2011-08-10  Gemma Barson  <gb10@sanger.ac.uk>
 Added 'gap' to supported GFF types
 src/seqtoolsUtils/blxGff3Parser.c | 3 +++
 src/seqtoolsUtils/blxmsp.h        | 1 +
 2 files changed, 4 insertions(+)

2011-08-09  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/utr' into develop
2011-08-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression with reading introns in exblx format
 src/seqtoolsUtils/blxparser.c | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

2011-08-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with constructing transcripts when given CDS/UTR components
 src/seqtoolsUtils/blxmsp.c | 259 +++++++++++++++++++++------------------------
 1 file changed, 123 insertions(+), 136 deletions(-)

2011-08-09  Gemma Barson  <gb10@sanger.ac.uk>
 RT225220: fixed a bug where multiple UTRs in the same exon are not displayed
 src/seqtoolsUtils/blxmsp.c    | 263 +++++++++++++++++++++++++-----------------
 src/seqtoolsUtils/utilities.c |   6 +
 src/seqtoolsUtils/utilities.h |   1 +
 3 files changed, 167 insertions(+), 103 deletions(-)

2011-08-08  Gemma Barson  <gb10@sanger.ac.uk>
 RT226652: fixed a bug where blixem was ignoring 'invalid' characters in fasta files
 src/seqtoolsUtils/blxparser.c | 15 ++++++++-------
 src/seqtoolsUtils/translate.c | 26 +++++++++++++++++---------
 src/seqtoolsUtils/utilities.c |  7 +++++++
 src/seqtoolsUtils/utilities.h |  1 +
 4 files changed, 33 insertions(+), 16 deletions(-)

2011-08-02  Gemma Barson  <gb10@sanger.ac.uk>
 Updated blixem what's new page
 src/doc/User_doc/blixem_news.html | 11 +++++++++++
 1 file changed, 11 insertions(+)

2011-08-02  Gemma Barson  <gb10@sanger.ac.uk>
 Updated Belvu documentation
 src/doc/Design_notes/index.html              |  2 +-
 src/doc/User_doc/Makefile.am                 |  4 +-
 src/doc/User_doc/belvu_news.html             | 17 +++++-
 src/doc/User_doc/belvu_quick_start.html      | 77 +++++++++++++++++-----------
 src/doc/User_doc/belvu_usage.txt             |  1 -
 src/doc/User_doc/blixem_quick_start.html     |  5 +-
 src/doc/User_doc/dotter_quick_start.html     |  5 +-
 src/doc/{Design_notes => User_doc}/todo.html |  6 ++-
 8 files changed, 73 insertions(+), 44 deletions(-)

2011-08-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a potential crash when opening the tree window if the user scrolls the mouse-wheel at the same time
 src/belvuApp/belvuTree.c | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

2011-07-29  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where user could not re-select the sort-by-similarity/id option after changing the selection
 src/belvuApp/belvuWindow.c | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

2011-07-29  Gemma Barson  <gb10@sanger.ac.uk>
 Added a fix to make sure tree cannot get so large that it causes a crash
 src/belvuApp/belvuTree.c | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

2011-07-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with sorting by similarity on start up when the first line is a markup line
 src/belvuApp/belvuMain.c | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

2011-07-28  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/belvu'
2011-07-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression with the output-probabilities function
 src/belvuApp/belvu.c | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

2011-07-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some leaks and memory bugs to do with the tree nodes
 src/belvuApp/belvu.c          |   1 -
 src/belvuApp/belvuTree.c      | 126 ++++++++++++++++++++----------------------
 src/belvuApp/belvu_.h         |   1 -
 src/seqtoolsUtils/utilities.c |   3 +
 4 files changed, 64 insertions(+), 67 deletions(-)

2011-07-27  Gemma Barson  <gb10@sanger.ac.uk>
 A Tree struct is now used to provide a persistent pointer to the main tree
 src/belvuApp/belvu.c       |  61 +++++++++-----
 src/belvuApp/belvuMain.c   |   9 +-
 src/belvuApp/belvuTree.c   | 203 +++++++++++++++++++++++++++------------------
 src/belvuApp/belvuTree.h   |   5 +-
 src/belvuApp/belvuWindow.c |  10 +--
 src/belvuApp/belvu_.h      |  46 +++++-----
 6 files changed, 201 insertions(+), 133 deletions(-)

2011-07-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with displaying bootstrap trees
 src/belvuApp/belvu.c       |  50 ++++++--
 src/belvuApp/belvuTree.c   | 314 ++++++++++++++++++++++++++++++++++-----------
 src/belvuApp/belvuTree.h   |   8 +-
 src/belvuApp/belvuWindow.c |  74 +++--------
 4 files changed, 307 insertions(+), 139 deletions(-)

2011-07-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the blosum matrix when calculating the tree
 src/belvuApp/belvuTree.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-07-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with bootstrap trees
 src/belvuApp/belvu.c       |  4 ++--
 src/belvuApp/belvuMain.c   |  2 +-
 src/belvuApp/belvuTree.c   | 53 ++++++++++++++++++++++++++++++++--------------
 src/belvuApp/belvuWindow.c |  2 +-
 src/belvuApp/belvu_.h      |  2 +-
 5 files changed, 42 insertions(+), 21 deletions(-)

2011-07-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with sorting by similarity
 src/belvuApp/belvu.c          | 71 +++++++++++++++++++++++++++++++++----------
 src/belvuApp/belvuAlignment.c |  6 ++--
 src/belvuApp/belvuAlignment.h |  3 ++
 src/belvuApp/belvuMain.c      |  6 ++++
 src/belvuApp/belvuTree.c      |  2 +-
 5 files changed, 67 insertions(+), 21 deletions(-)

2011-07-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where the initial sort mode was not being reflected in the menu options
 src/belvuApp/belvuWindow.c | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

2011-07-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with sorting by identity
 src/belvuApp/belvu.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-07-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with disabling colors
 src/belvuApp/belvuAlignment.c | 11 +++++++++++
 src/belvuApp/belvuWindow.c    | 11 +++++++++--
 2 files changed, 20 insertions(+), 2 deletions(-)

2011-07-22  Gemma Barson  <gb10@sanger.ac.uk>
 Alignment pointers are now persistent (fixes lots of bugs to do with invalid pointers)
 src/belvuApp/belvu.c          | 526 +++++++++++++++++-------------------------
 src/belvuApp/belvuAlignment.c |  10 +-
 src/belvuApp/belvuMain.c      |  39 ++--
 src/belvuApp/belvuTree.c      |  86 ++-----
 src/belvuApp/belvuWindow.c    |  12 +-
 src/belvuApp/belvu_.h         |   2 +
 6 files changed, 252 insertions(+), 423 deletions(-)

2011-07-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression with the --zoom-range argument
 src/blixemApp/blxwindow.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2011-07-22  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem now gets the reference sequence coords from the fasta definition line, rather than the sequence-region header in the GFF file
 src/blixemApp/blixem_.h           |  2 +-
 src/blixemApp/blxmain.c           | 35 +++++++++++-----
 src/blixemApp/blxview.c           |  3 +-
 src/dotterApp/dotterMain.c        |  3 +-
 src/seqtoolsUtils/blxGff3Parser.c | 30 ++++++++++----
 src/seqtoolsUtils/blxGff3Parser.h |  2 +-
 src/seqtoolsUtils/blxparser.c     | 84 +++++++++++++++++++++++++--------------
 7 files changed, 105 insertions(+), 54 deletions(-)

2011-07-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the --zoom-range argument in protein blixem
 src/blixemApp/bigpicture.c | 5 +----
 src/blixemApp/blxwindow.c  | 5 +++++
 2 files changed, 6 insertions(+), 4 deletions(-)

2011-07-21  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/belvu'
2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with sorting by tree on startup
 src/belvuApp/belvu.c       | 26 +++++++++++++++++---------
 src/belvuApp/belvuMain.c   |  2 +-
 src/belvuApp/belvuWindow.c |  6 +++---
 src/belvuApp/belvu_.h      |  4 ++--
 4 files changed, 23 insertions(+), 15 deletions(-)

2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where markup lines are not shown if tree is shown on startup
 src/belvuApp/belvuWindow.c | 4 ++++
 1 file changed, 4 insertions(+)

2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Removed obsolete debugging option
 src/belvuApp/belvuMain.c | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where the markup colors file could overwrite the residue colors file
 src/belvuApp/belvu.c       |  9 ++++++++-
 src/belvuApp/belvuMain.c   | 10 +++++-----
 src/belvuApp/belvuWindow.c |  2 +-
 src/belvuApp/belvu_.h      |  2 +-
 4 files changed, 15 insertions(+), 8 deletions(-)

2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where custom colors were being overwritten after loading a color file with the -l argument
 src/belvuApp/belvuMain.c   | 78 ++++++++++++++++++++--------------------------
 src/belvuApp/belvuWindow.c | 11 +++++--
 2 files changed, 42 insertions(+), 47 deletions(-)

2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the wrong conservation was being calculated when using the -c argument
 src/belvuApp/belvu.c | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the --zoom-range argument for protein blixem
 src/blixemApp/blxwindow.c | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/belvu'
2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added belvu_.h to autoconf (it was missing from the distribution)
 src/belvuApp/Makefile.am | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-07-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with the -b option
 src/belvuApp/belvu.c     | 84 +++++++++++++++++++++++++++++++++++++++++-------
 src/belvuApp/belvuMain.c |  4 +--
 src/belvuApp/belvuTree.c | 34 +++++++++++++-------
 src/belvuApp/belvu_.h    |  3 +-
 4 files changed, 100 insertions(+), 25 deletions(-)

2011-07-19  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a typo that was causing the initial exon view height to be calculated incorrectly
 src/blixemApp/blxwindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-07-19  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where introns that are partially out of range were not always being shown
 src/seqtoolsUtils/blxGff3Parser.c | 18 +++++++++++++++---
 src/seqtoolsUtils/blxmsp.c        |  5 +++++
 src/seqtoolsUtils/blxmsp.h        |  1 +
 3 files changed, 21 insertions(+), 3 deletions(-)

2011-07-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where short-reads were incorrectly squashed onto the same line when their sources are different
 src/blixemApp/detailviewtree.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

2011-07-18  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/belvu'
2011-07-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash with the -b argument
 src/belvuApp/belvuTree.c | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

2011-07-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a divide-by-zero error when using the -c argument
 src/belvuApp/belvuMain.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-07-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fix a potential crash if the tree size is too big
 src/belvuApp/belvuAlignment.c | 6 ++----
 src/belvuApp/belvuTree.c      | 8 +++++++-
 src/belvuApp/belvu_.h         | 3 +++
 3 files changed, 12 insertions(+), 5 deletions(-)

2011-07-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue with the tree scale updating on the tree settings dialog
 src/belvuApp/belvuTree.c | 26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

2011-07-17  Gemma Barson  <gb10@sanger.ac.uk>
 Update tree scale according to current tree method on tree settings dialog
 src/belvuApp/belvu.c     |   2 +-
 src/belvuApp/belvuTree.c | 123 +++++++++++++++++++++++++++++++++++++++--------
 src/belvuApp/belvuTree.h |   2 +
 3 files changed, 105 insertions(+), 22 deletions(-)

2011-07-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with uninitialised strings in markup lines when strip-coords option is off
 src/belvuApp/belvu.c | 1 +
 1 file changed, 1 insertion(+)

2011-07-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where the main window was being shown in tree-only mode
 src/belvuApp/belvuWindow.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

2011-07-17  Gemma Barson  <gb10@sanger.ac.uk>
 Another bugfix to do with separateMarkupLines
 src/belvuApp/belvuTree.c | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

2011-07-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed bugs with tree selection getting messed up by separateMarkupLines
 src/belvuApp/belvu.c       |  12 +++--
 src/belvuApp/belvuMain.c   |  40 +++++-----------
 src/belvuApp/belvuTree.c   | 116 ++++++++++++++++++++++++++++++++++-----------
 src/belvuApp/belvuWindow.c |  35 ++++++++++----
 src/belvuApp/belvu_.h      |   3 ++
 5 files changed, 137 insertions(+), 69 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Removed commented-out code
 src/belvuApp/belvuMain.c   |  24 --------
 src/belvuApp/belvuTree.c   |  13 ++--
 src/belvuApp/belvuWindow.c | 146 ++++++++-------------------------------------
 3 files changed, 31 insertions(+), 152 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Removed old compiled-out code
 src/belvuApp/belvu.c | 1942 +-------------------------------------------------
 1 file changed, 21 insertions(+), 1921 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Small cosmetic changes to menus
 src/belvuApp/belvuWindow.c | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a program error where messages could get directed to the wrong output
 src/seqtoolsUtils/utilities.c | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Info messages and warnings/errors are now sent to stderr
 src/belvuApp/belvu.c          | 42 +++++++++++++------------------------
 src/belvuApp/belvuMain.c      | 15 ++++++++++++--
 src/belvuApp/belvuTree.c      |  8 ++++----
 src/belvuApp/belvuWindow.c    | 10 ++++-----
 src/seqtoolsUtils/utilities.c | 48 +++++++++++++++++++++++++------------------
 5 files changed, 64 insertions(+), 59 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where the conservation plot line width was not being used
 src/belvuApp/belvuConsPlot.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying
 src/belvuApp/belvu.c | 62 +---------------------------------------------------
 1 file changed, 1 insertion(+), 61 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where branch labels where not shown in centre of branch
 src/belvuApp/belvuTree.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed highlighting for match segments
 src/belvuApp/belvuAlignment.c |  3 ---
 src/belvuApp/belvuTree.c      | 14 ++++++++------
 2 files changed, 8 insertions(+), 9 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with reading matching segments
 src/belvuApp/belvu.c          | 499 +-----------------------------------------
 src/belvuApp/belvuAlignment.c |  11 +-
 2 files changed, 11 insertions(+), 499 deletions(-)

2011-07-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where the busy cursor was not being updated
 src/belvuApp/belvu.c | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

2011-07-14  Gemma Barson  <gb10@sanger.ac.uk>
 Tidying code
 src/belvuApp/belvu.c | 71 ++--------------------------------------------------
 1 file changed, 2 insertions(+), 69 deletions(-)

2011-07-14  Gemma Barson  <gb10@sanger.ac.uk>
 Added busy cursor when outputting identities and calculating tree
 src/belvuApp/belvu.c       | 45 +++++++++++++++++++++++++++++++++++++++++++++
 src/belvuApp/belvuMain.c   |  2 +-
 src/belvuApp/belvuTree.c   |  3 ++-
 src/belvuApp/belvuWindow.c | 18 ++++++++----------
 src/belvuApp/belvu_.h      |  6 ++++++
 5 files changed, 62 insertions(+), 12 deletions(-)

2011-07-14  Gemma Barson  <gb10@sanger.ac.uk>
 Replaced color picker buttons with plain color boxes
 src/belvuApp/belvuWindow.c | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

2011-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where foreground colors were not being shown
 src/belvuApp/belvuAlignment.c | 97 ++++++++++++++++++++++++-------------------
 src/seqtoolsUtils/utilities.c |  9 ++++
 src/seqtoolsUtils/utilities.h |  1 +
 3 files changed, 65 insertions(+), 42 deletions(-)

2011-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a potential crash where the wrapped-alignment pixmap is too large
 src/belvuApp/belvuAlignment.c | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

2011-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 Made the organisms window scrollable
 src/belvuApp/belvu.c       |   1 +
 src/belvuApp/belvuWindow.c | 149 +++++++++++++++++++++++++++++----------------
 src/belvuApp/belvu_.h      |   1 +
 3 files changed, 98 insertions(+), 53 deletions(-)

2011-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 Removed an incorrect shortcut tip
 src/belvuApp/belvuWindow.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2011-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the scoredist calculation being based on invalid values
 src/belvuApp/belvuTree.c | 46 ++++++++++++++++++++++++----------------------
 1 file changed, 24 insertions(+), 22 deletions(-)

2011-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Removed debug statement
 src/seqtoolsUtils/utilities.h | 2 --
 1 file changed, 2 deletions(-)

2011-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Create/show the tree after OK-ing the tree settings dialog
 src/belvuApp/belvuTree.c | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

2011-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed another rounding error and tidied tree code
 src/belvuApp/belvu.c          |  15 +-
 src/belvuApp/belvuTree.c      | 485 ++++++++++++++++++++++++------------------
 src/seqtoolsUtils/utilities.h |   3 +
 3 files changed, 279 insertions(+), 224 deletions(-)

2011-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a rounding error
 src/belvuApp/belvuTree.c | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

2011-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where wrapped-alignment font was not being set
 src/belvuApp/belvuWindow.c | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

2011-07-11  Gemma Barson  <gb10@sanger.ac.uk>
 Updated help and usage info
 src/belvuApp/belvuMain.c                | 3 ++-
 src/doc/User_doc/belvu_quick_start.html | 3 +++
 src/doc/User_doc/belvu_usage.txt        | 1 +
 3 files changed, 6 insertions(+), 1 deletion(-)

2011-07-08  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with the font-size environment variable
 src/belvuApp/belvuWindow.c | 23 ++++++++---------------
 1 file changed, 8 insertions(+), 15 deletions(-)

2011-07-08  Gemma Barson  <gb10@sanger.ac.uk>
 Allow tree and alignment to zoom separately
 src/belvuApp/belvuTree.c      | 25 ++++++++++++++++++++-----
 src/belvuApp/belvuWindow.c    | 28 +---------------------------
 src/belvuApp/belvuWindow.h    |  2 --
 src/seqtoolsUtils/utilities.c | 12 ++++++++++++
 src/seqtoolsUtils/utilities.h |  1 +
 5 files changed, 34 insertions(+), 34 deletions(-)

2011-07-08  Gemma Barson  <gb10@sanger.ac.uk>
 Added zoom buttons and shortcut keys
 src/belvuApp/belvuAlignment.c |   9 ----
 src/belvuApp/belvuAlignment.h |   2 -
 src/belvuApp/belvuTree.c      |  60 +++++++++++++++++++--
 src/belvuApp/belvuTree.h      |   1 +
 src/belvuApp/belvuWindow.c    | 119 +++++++++++++++++++++++++++++++++---------
 src/belvuApp/belvuWindow.h    |   5 ++
 src/seqtoolsUtils/utilities.c |  16 ++++++
 src/seqtoolsUtils/utilities.h |   1 +
 8 files changed, 172 insertions(+), 41 deletions(-)

2011-07-08  Gemma Barson  <gb10@sanger.ac.uk>
 Added an option to change the menu font size
 src/belvuApp/belvuAlignment.c | 160 +++++++++++++++++++++++++++++-------------
 src/belvuApp/belvuAlignment.h |   4 ++
 src/belvuApp/belvuWindow.c    | 123 +++++++++++++++++++++++++++-----
 src/blixemApp/detailview.c    |   2 -
 src/seqtoolsUtils/utilities.h |   2 +
 5 files changed, 224 insertions(+), 67 deletions(-)

2011-07-07  Gemma Barson  <gb10@sanger.ac.uk>
 Added Find functionality
 src/belvuApp/belvu.c          |   8 ++
 src/belvuApp/belvuAlignment.c |  22 -----
 src/belvuApp/belvuWindow.c    | 200 +++++++++++++++++++++++++++++++++++++++++-
 src/belvuApp/belvu_.h         |   6 +-
 src/blixemApp/blxwindow.c     | 128 ---------------------------
 src/seqtoolsUtils/utilities.c | 126 ++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |  15 +++-
 7 files changed, 348 insertions(+), 157 deletions(-)

2011-07-07  Gemma Barson  <gb10@sanger.ac.uk>
 Updated belvu release notes
 src/doc/User_doc/belvu_news.html | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

2011-07-07  Gemma Barson  <gb10@sanger.ac.uk>
 Improved functionality to find external commands
 src/seqtoolsUtils/utilities.c | 41 +++++------------------------------------
 1 file changed, 5 insertions(+), 36 deletions(-)

2011-07-06  Gemma Barson  <gb10@sanger.ac.uk>
 Added new CGPH color scheme to default list
 src/belvuApp/belvu.c       | 16 ++++++++++++++--
 src/belvuApp/belvuWindow.c |  6 ++++--
 src/belvuApp/belvu_.h      |  3 ++-
 3 files changed, 20 insertions(+), 5 deletions(-)

2011-07-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where the toggle-color-modes option was not updating the current color-scheme in the menu
 src/belvuApp/belvuWindow.c | 50 +++++++++++++++++++---------------------------
 1 file changed, 21 insertions(+), 29 deletions(-)

2011-07-06  Gemma Barson  <gb10@sanger.ac.uk>
 Copy the selected sequence name to the primary buffer
 src/belvuApp/belvuWindow.c | 3 +++
 1 file changed, 3 insertions(+)

2011-07-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue with updates following remove-by-conservation
 src/belvuApp/belvuWindow.c | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

2011-07-06  Gemma Barson  <gb10@sanger.ac.uk>
 Show the tree when the sort-by-tree option is selected
 src/belvuApp/belvu.c | 6 ++++++
 1 file changed, 6 insertions(+)

2011-07-06  Gemma Barson  <gb10@sanger.ac.uk>
 Better handling of tree recalculations
 src/belvuApp/belvuTree.c   |  30 ++++----
 src/belvuApp/belvuWindow.c | 170 ++++++++++++++++++++++-----------------------
 2 files changed, 101 insertions(+), 99 deletions(-)

2011-07-06  Gemma Barson  <gb10@sanger.ac.uk>
 Added keyboard shortcut for toggling color mode
 src/belvuApp/belvuWindow.c | 2 ++
 1 file changed, 2 insertions(+)

2011-07-06  Gemma Barson  <gb10@sanger.ac.uk>
 The conservation plot is now automatically updated after sequences or columns are deleted
 src/belvuApp/belvu.c          |  7 ++++++-
 src/belvuApp/belvuAlignment.c |  1 +
 src/belvuApp/belvuConsPlot.c  | 27 +++++++++++++++++----------
 src/belvuApp/belvuConsPlot.h  |  5 +++--
 4 files changed, 27 insertions(+), 13 deletions(-)

2011-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Improved color-scheme toggle methods
 src/belvuApp/belvuWindow.c    | 67 +++++++++++++++++++++++--------------------
 src/belvuApp/belvu_.h         | 20 ++++++-------
 src/seqtoolsUtils/utilities.c | 20 +++++++++++++
 src/seqtoolsUtils/utilities.h |  1 +
 4 files changed, 66 insertions(+), 42 deletions(-)

2011-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Separated color sub-menus into separate color schemes menu
 src/belvuApp/belvu.c       |  7 +++++-
 src/belvuApp/belvuWindow.c | 56 ++++++++++++++++++++++------------------------
 2 files changed, 33 insertions(+), 30 deletions(-)

2011-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Updated to-do notes for Belvu
 src/doc/Design_notes/todo.html | 55 +++++++++++++++++++++++++++++++++---------
 1 file changed, 44 insertions(+), 11 deletions(-)

2011-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Improved status logging when calling the fetch command
 src/belvuApp/belvu.c          | 11 +++++++----
 src/seqtoolsUtils/utilities.c |  4 ++--
 2 files changed, 9 insertions(+), 6 deletions(-)

2011-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Added a settings dialog to enable user to change conservation-plot properties
 src/belvuApp/belvuConsPlot.c  | 115 +++++++++++++++++++++++++++++++++++++-----
 src/belvuApp/belvuWindow.c    |   4 +-
 src/blixemApp/blxwindow.c     |  18 +++----
 src/dotterApp/dotter.c        |  62 -----------------------
 src/seqtoolsUtils/utilities.c |  77 ++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |  20 ++++++++
 6 files changed, 210 insertions(+), 86 deletions(-)

2011-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the conservation plot where the average line label was not shown
 src/belvuApp/belvuConsPlot.c  | 19 +++++++++++--------
 src/belvuApp/belvuTree.c      | 15 ---------------
 src/seqtoolsUtils/utilities.c | 38 ++++++++++++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |  3 +++
 4 files changed, 52 insertions(+), 23 deletions(-)

2011-07-05  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed bugs with conservation plot
 src/belvuApp/belvuConsPlot.c | 213 ++++++++++++++++++++-----------------------
 1 file changed, 97 insertions(+), 116 deletions(-)

2011-07-04  Gemma Barson  <gb10@sanger.ac.uk>
 Added test notes for belvu
 src/doc/Design_notes/testing.ods | Bin 35579 -> 36754 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2011-07-04  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: conservation plot is now working
 src/belvuApp/belvuConsPlot.c | 314 ++++++++++++++++++++++++++++++-------------
 src/belvuApp/belvuConsPlot.h |   4 +-
 src/belvuApp/belvuWindow.c   |  10 +-
 src/belvuApp/belvu_.h        |   1 +
 4 files changed, 234 insertions(+), 95 deletions(-)

2011-07-01  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: implemented conservation plot
 src/belvuApp/belvu.c         | 148 -------------------------
 src/belvuApp/belvuConsPlot.c | 254 +++++++++++++++++++++++++++++++++----------
 src/belvuApp/belvuWindow.c   |   4 +
 src/belvuApp/belvu_.h        |   4 +-
 4 files changed, 206 insertions(+), 204 deletions(-)

2011-07-01  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: moved conservtion plot code to separate file
 src/belvuApp/Makefile.am     |   6 +-
 src/belvuApp/belvuConsPlot.c | 281 +++++++++++++++++++++++++++++++++++++++++++
 src/belvuApp/belvuConsPlot.h |  44 +++++++
 src/belvuApp/belvuWindow.c   | 118 +-----------------
 src/belvuApp/belvu_.h        |   2 +
 5 files changed, 337 insertions(+), 114 deletions(-)

2011-07-01  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: Added conservation plot window
 src/belvuApp/belvuAlignment.c | 135 ++++++++++++++++++++--------------
 src/belvuApp/belvuAlignment.h |  21 +++---
 src/belvuApp/belvuWindow.c    | 163 ++++++++++++++++++++++++++++++++++++------
 src/belvuApp/belvu_.h         |   1 +
 src/seqtoolsUtils/utilities.c |  61 ++++++++++++++++
 src/seqtoolsUtils/utilities.h |  12 ++++
 6 files changed, 308 insertions(+), 85 deletions(-)

2011-06-29  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with the wrapped-alignment view
 src/belvuApp/belvuAlignment.c | 79 ++++++++++++++++++++++++++++---------------
 1 file changed, 52 insertions(+), 27 deletions(-)

2011-06-29  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed issues with quit not prompting to save when called from spawned windows
 src/belvuApp/belvuAlignment.c |  4 ++--
 src/belvuApp/belvuWindow.c    | 23 ++++++++++++++++++++++-
 2 files changed, 24 insertions(+), 3 deletions(-)

2011-06-29  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where the feedback box wasn't being updated when the row selection changes
 src/belvuApp/belvuWindow.c | 58 +++++++++++++++++++++++++---------------------
 1 file changed, 31 insertions(+), 27 deletions(-)

2011-06-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with removing sequences messing up the array
 src/belvuApp/belvu.c       | 45 ++++++++++++++++++++-----------------------
 src/belvuApp/belvuWindow.c | 48 +++++++++++++++++++++++++---------------------
 2 files changed, 47 insertions(+), 46 deletions(-)

2011-06-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with markup lines appearing in the tree when the tree is created using 'calculate tree'
 src/belvuApp/belvuWindow.c | 3 +++
 1 file changed, 3 insertions(+)

2011-06-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the tree was incorrectly showing markup lines
 src/belvuApp/belvuTree.c | 3 +++
 1 file changed, 3 insertions(+)

2011-06-27  Gemma Barson  <gb10@sanger.ac.uk>
 Updated Belvu documentation and release notes
 src/doc/User_doc/belvu_news.html        | 11 ++++++++++
 src/doc/User_doc/belvu_quick_start.html | 39 ++++++++++++++++++++-------------
 2 files changed, 35 insertions(+), 15 deletions(-)

2011-06-27  Gemma Barson  <gb10@sanger.ac.uk>
 Added --help command-line argument
 src/belvuApp/belvuMain.c         | 14 ++++++++++----
 src/doc/User_doc/belvu_usage.txt |  3 +++
 2 files changed, 13 insertions(+), 4 deletions(-)

2011-06-27  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented annotations window
 src/belvuApp/belvu.c          | 41 -------------------------
 src/belvuApp/belvuMain.c      |  2 +-
 src/belvuApp/belvuWindow.c    | 69 +++++++++++++++++++++++++++++++++++++++++--
 src/belvuApp/belvuWindow.h    |  1 +
 src/belvuApp/belvu_.h         |  1 -
 src/blixemApp/detailview.c    | 25 ----------------
 src/blixemApp/detailview.h    |  1 -
 src/seqtoolsUtils/utilities.c | 25 ++++++++++++++++
 src/seqtoolsUtils/utilities.h |  1 +
 9 files changed, 95 insertions(+), 71 deletions(-)

2011-06-27  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented mouse-wheel scrolling for label areas as well as main alignment area
 src/belvuApp/belvuAlignment.c | 28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

2011-06-27  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented mouse-wheel scrolling
 src/belvuApp/belvuAlignment.c | 64 +++++++++++++++++++++++++++++++++++++------
 1 file changed, 55 insertions(+), 9 deletions(-)

2011-06-24  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented fetch
 src/belvuApp/belvu.c          | 122 ++++++++++++++++++++++++++----------------
 src/belvuApp/belvuAlignment.c |  12 ++++-
 src/belvuApp/belvuWindow.c    |  14 +++++
 src/belvuApp/belvu_.h         |   3 ++
 src/blixemApp/blxFetch.c      | 112 +++-----------------------------------
 src/seqtoolsUtils/utilities.c | 120 ++++++++++++++++++++++++++++++++++++++++-
 src/seqtoolsUtils/utilities.h |   7 ++-
 7 files changed, 237 insertions(+), 153 deletions(-)

2011-06-23  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'output score' menu option
 src/belvuApp/belvu.c       | 16 ----------------
 src/belvuApp/belvuWindow.c | 17 +++++++++++++++++
 2 files changed, 17 insertions(+), 16 deletions(-)

2011-06-23  Gemma Barson  <gb10@sanger.ac.uk>
 Improved error-handling when reading scores file
 src/belvuApp/belvuAlignment.c |  5 ++++-
 src/belvuApp/belvuMain.c      | 34 +++++++++++++++++++++++++++++-----
 2 files changed, 33 insertions(+), 6 deletions(-)

2011-06-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the wrapped-alignment view
 src/belvuApp/belvuAlignment.c | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

2011-06-23  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented organisms window
 src/belvuApp/belvuWindow.c | 199 +++++++++++++++++++++++++++++++++++++++------
 1 file changed, 173 insertions(+), 26 deletions(-)

2011-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Orthologs are now highlighted in the tree after 'find orthologs' option is called
 src/belvuApp/belvu.c       |  1 +
 src/belvuApp/belvuTree.c   | 44 ++++++++++++++++++++++++++++++++++++--------
 src/belvuApp/belvuTree.h   |  2 +-
 src/belvuApp/belvuWindow.c | 17 ++++++++++++++---
 src/belvuApp/belvu_.h      |  3 ++-
 5 files changed, 54 insertions(+), 13 deletions(-)

2011-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'find orthologs' option, and made some changes to the way action groups are handled
 src/belvuApp/belvu.c       | 117 ++++++++++++++-------------
 src/belvuApp/belvuTree.c   |  68 ++++++++++++++--
 src/belvuApp/belvuTree.h   |   8 +-
 src/belvuApp/belvuWindow.c | 191 ++++++++++++++++++++++++++++-----------------
 src/belvuApp/belvuWindow.h |   2 +
 src/belvuApp/belvu_.h      |   5 +-
 6 files changed, 250 insertions(+), 141 deletions(-)

2011-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Small fix to recalculate name column size when sequences are deleted
 src/belvuApp/belvuAlignment.c | 5 +++++
 1 file changed, 5 insertions(+)

2011-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Made the 'remove many sequences' option a toggle option, so you can click again to turn it off
 src/belvuApp/belvu.c       |  1 +
 src/belvuApp/belvuWindow.c | 61 +++++++++++++++++++++++++---------------------
 src/belvuApp/belvu_.h      |  3 ++-
 3 files changed, 36 insertions(+), 29 deletions(-)

2011-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'save tree' option
 src/belvuApp/belvu.c       | 77 ++++++++++++++++------------------------------
 src/belvuApp/belvuMain.c   |  2 +-
 src/belvuApp/belvuTree.c   |  2 +-
 src/belvuApp/belvuWindow.c | 53 ++++++++++++++++++++++++++++---
 src/belvuApp/belvu_.h      |  2 +-
 5 files changed, 79 insertions(+), 57 deletions(-)

2011-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to the toolbar and menu
 src/belvuApp/belvuWindow.c    | 71 +++++++++++++++++++++----------------------
 src/blixemApp/detailview.c    |  4 +--
 src/seqtoolsUtils/utilities.c |  7 +++--
 src/seqtoolsUtils/utilities.h |  2 +-
 4 files changed, 41 insertions(+), 43 deletions(-)

2011-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the mean score was incorrect when alignment contains markup lines
 src/belvuApp/belvu.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2011-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where scores were being calculated for markup lines
 src/belvuApp/belvu.c | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

2011-06-22  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'compare all' menu option
 src/belvuApp/belvu.c       | 135 +++++++++++++++++++++++++++------------------
 src/belvuApp/belvuWindow.c |   8 ++-
 src/belvuApp/belvu_.h      |   2 +
 3 files changed, 88 insertions(+), 57 deletions(-)

2011-06-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added --version and --compiled arguments
 src/belvuApp/belvuMain.c | 286 +++++++++++++++++++++++++++--------------------
 1 file changed, 167 insertions(+), 119 deletions(-)

2011-06-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added minor tickmarks to scale
 src/belvuApp/belvuAlignment.c | 63 +++++++++++++++++++++++--------------------
 1 file changed, 34 insertions(+), 29 deletions(-)

2011-06-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added keyboard shortcuts
 src/belvuApp/belvuAlignment.c |  87 +++++++++++++++++++++
 src/belvuApp/belvuAlignment.h |   7 ++
 src/belvuApp/belvuWindow.c    | 177 ++++++++++++++++++++++++++++++++++--------
 3 files changed, 239 insertions(+), 32 deletions(-)

2011-06-21  Gemma Barson  <gb10@sanger.ac.uk>
 Improved performance of drawing alignments
 src/belvuApp/belvuAlignment.c | 54 +++++++++++++++++++++++++++----------------
 1 file changed, 34 insertions(+), 20 deletions(-)

2011-06-21  Gemma Barson  <gb10@sanger.ac.uk>
 Improved performance of middle-dragging
 src/belvuApp/belvuAlignment.c | 67 +++++++++++++++++++++++++++++++++++++++----
 src/belvuApp/belvuAlignment.h |  1 +
 src/belvuApp/belvuWindow.c    | 11 +++----
 src/belvuApp/belvu_.h         |  2 ++
 4 files changed, 70 insertions(+), 11 deletions(-)

2011-06-21  Gemma Barson  <gb10@sanger.ac.uk>
 Updated colours to be the same as the old belvu colours
 src/belvuApp/belvu.c | 78 +++++++++++++++++++++++++++-------------------------
 1 file changed, 41 insertions(+), 37 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where rows were being highlighted incorrectly
 src/belvuApp/belvuAlignment.c | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added prompt to save the alignment if it has been edited when the users quits
 src/belvuApp/belvuWindow.c | 83 +++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 78 insertions(+), 5 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Right-align column text
 src/belvuApp/belvu.c          | 39 +++++++++++++++++++++++++++++++++++++--
 src/belvuApp/belvuAlignment.c | 25 +++++++++++--------------
 src/belvuApp/belvu_.h         |  3 ++-
 3 files changed, 50 insertions(+), 17 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added header for alignment display area
 src/belvuApp/belvuAlignment.c | 250 +++++++++++++++++++++++++++++++++---------
 1 file changed, 197 insertions(+), 53 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with incorrect drawing of final blank row
 src/belvuApp/belvuAlignment.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where extra rows were being drawn unnecessarily
 src/belvuApp/belvuAlignment.c | 52 ++++++++++++++++++++++++++++++++-----------
 1 file changed, 39 insertions(+), 13 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with row selections
 src/belvuApp/belvuAlignment.c | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added summary label at top of headers column
 src/belvuApp/belvuAlignment.c | 27 ++++++++++++++++++++++-----
 1 file changed, 22 insertions(+), 5 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed issues with the scroll ranges not updated when rows/columns are deleted
 src/belvuApp/belvuAlignment.c | 34 +++++++++++++++++++++-------------
 1 file changed, 21 insertions(+), 13 deletions(-)

2011-06-20  Gemma Barson  <gb10@sanger.ac.uk>
 Finished work to implement a custom vertical scrollbar
 src/belvuApp/belvuAlignment.c | 47 +++++++++++++++++++------------------------
 1 file changed, 21 insertions(+), 26 deletions(-)

2011-06-17  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: Performance improvements: only draw alignments that are in the scroll range
 src/belvuApp/belvuAlignment.c | 176 +++++++++++++++++++++++++++++-------------
 1 file changed, 122 insertions(+), 54 deletions(-)

2011-06-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where 'show tree' was not presenting the tree if it had to create it first
 src/belvuApp/belvuWindow.c | 34 ++++++++++++++++------------------
 1 file changed, 16 insertions(+), 18 deletions(-)

2011-06-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some merge errors
 src/seqtoolsUtils/utilities.c | 36 ------------------------------------
 src/seqtoolsUtils/utilities.h |  5 -----
 2 files changed, 41 deletions(-)

2011-06-15  Gemma Barson  <gb10@sanger.ac.uk>
 Moved some utility functions to utils library
 src/belvuApp/belvuWindow.c    | 32 --------------------------------
 src/seqtoolsUtils/utilities.c | 37 +++++++++++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |  3 +++
 3 files changed, 40 insertions(+), 32 deletions(-)

2011-06-09  Gemma Barson  <gb10@sanger.ac.uk>
 Save dialog now remembers the name and directory
 src/belvuApp/belvu.c       |  4 ++--
 src/belvuApp/belvuMain.c   | 25 +++++++++++++---------
 src/belvuApp/belvuWindow.c | 53 +++++++++++++++++++++++++++++++++++++---------
 src/belvuApp/belvu_.h      |  4 ++--
 4 files changed, 62 insertions(+), 24 deletions(-)

2011-06-09  Gemma Barson  <gb10@sanger.ac.uk>
 Added toggle boxes to save-as dialog to allow user to change separator char
 src/belvuApp/belvuWindow.c | 49 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

2011-06-09  Gemma Barson  <gb10@sanger.ac.uk>
 Added 'save coords' option to save as dialog
 src/belvuApp/belvuWindow.c | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

2011-06-09  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented save-as dialog
 src/belvuApp/belvu.c       | 45 ++++++++++++-----------
 src/belvuApp/belvuMain.c   | 12 ++++---
 src/belvuApp/belvuWindow.c | 90 ++++++++++++++++++++++++++++++++++++++++------
 src/belvuApp/belvu_.h      | 23 ++++++++----
 4 files changed, 125 insertions(+), 45 deletions(-)

2011-06-09  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented option to save Mul files
 src/belvuApp/belvu.c       | 787 +++++++--------------------------------------
 src/belvuApp/belvuMain.c   |   2 +-
 src/belvuApp/belvuWindow.c |  64 +++-
 src/belvuApp/belvu_.h      |   4 +-
 4 files changed, 189 insertions(+), 668 deletions(-)

2011-06-08  Gemma Barson  <gb10@sanger.ac.uk>
 Display score column if scores are enabled
 src/belvuApp/belvuAlignment.c | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

2011-06-08  Gemma Barson  <gb10@sanger.ac.uk>
 Don't draw coords for markup rows
 src/belvuApp/belvuAlignment.c | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

2011-06-08  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the wrapped view for selex data
 src/belvuApp/belvuAlignment.c | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

2011-06-08  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented selex file parsing
 src/belvuApp/belvu.c          | 665 ++++++++++++++++++++++++------------------
 src/belvuApp/belvuAlignment.c | 118 +++++---
 src/belvuApp/belvuTree.c      |  15 +-
 src/belvuApp/belvuWindow.c    |  16 +-
 src/belvuApp/belvu_.h         |   8 +-
 5 files changed, 480 insertions(+), 342 deletions(-)

2011-06-08  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed bugs with reading MSF files
 src/belvuApp/belvu.c | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

2011-06-08  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented hide/unhide options
 src/belvuApp/belvu.c          | 23 -----------------------
 src/belvuApp/belvuAlignment.c | 41 ++++++++++++++++++++++++++++++++++++-----
 src/belvuApp/belvuWindow.c    | 23 +++++++++++++++++++++++
 src/belvuApp/belvu_.h         |  4 ++--
 4 files changed, 61 insertions(+), 30 deletions(-)

2011-06-08  Gemma Barson  <gb10@sanger.ac.uk>
 Added more toolbar items
 src/belvuApp/belvuWindow.c | 27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

2011-06-08  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to remove-columns-by-conservation dialog
 src/belvuApp/belvuWindow.c | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

2011-06-07  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'select gap character' option
 src/belvuApp/belvu.c       |  1 +
 src/belvuApp/belvuWindow.c | 77 +++++++++++++++++++++++++++++++++++++++++++++-
 src/belvuApp/belvu_.h      |  1 +
 3 files changed, 78 insertions(+), 1 deletion(-)

2011-06-07  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'read labels' menu option
 src/belvuApp/belvu.c       | 132 +++++++++++++++++++++++----------------------
 src/belvuApp/belvuWindow.c |  21 ++++++++
 src/belvuApp/belvu_.h      |   1 +
 3 files changed, 90 insertions(+), 64 deletions(-)

2011-06-07  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying (menu action lists)
 src/belvuApp/belvuWindow.c | 204 +++++++++++++++++++++++++++++----------------
 1 file changed, 132 insertions(+), 72 deletions(-)

2011-06-07  Gemma Barson  <gb10@sanger.ac.uk>
 Postfix menu options with ... if the action has a prompt
 src/belvuApp/belvuWindow.c | 46 +++++++++++++++++++++++-----------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

2011-06-07  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'remove gappy columns' menu option
 src/belvuApp/belvuWindow.c | 58 ++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 48 insertions(+), 10 deletions(-)

2011-06-07  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where the fasta file name was incorrectly including the '>' marker
 src/seqtoolsUtils/blxparser.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the remove-columns-by-conservation dialog
 src/belvuApp/belvuWindow.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2011-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'auto remove empty columns' menu option
 src/belvuApp/belvu.c       |  2 ++
 src/belvuApp/belvuWindow.c | 13 +++++++++++--
 src/belvuApp/belvu_.h      |  2 +-
 3 files changed, 14 insertions(+), 3 deletions(-)

2011-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented option to remove columns by conservation
 src/belvuApp/belvu.c       | 98 ++++++++++++++++++++--------------------------
 src/belvuApp/belvuWindow.c | 85 +++++++++++++++++++++++++++++++++++++++-
 src/belvuApp/belvu_.h      |  2 +
 3 files changed, 129 insertions(+), 56 deletions(-)

2011-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash when clicking on an empty row
 src/belvuApp/belvuWindow.c | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

2011-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Updated usage text
 src/belvuApp/belvuMain.c          |  60 +++++++++------
 src/belvuApp/belvu_.h             |   6 +-
 src/blixemApp/blixem_.h           |   2 +-
 src/blixemApp/blxmain.c           |   7 +-
 src/doc/User_doc/belvu_usage.txt  | 154 ++++++++++++++++++++------------------
 src/doc/User_doc/blixem_usage.txt |  95 +++++++++++++++++++++++
 src/doc/User_doc/dotter_usage.txt |  13 ++++
 src/dotterApp/dotterMain.c        |   2 +-
 src/dotterApp/dotter_.h           |   2 +-
 src/seqtoolsUtils/version.h       |   2 +-
 10 files changed, 236 insertions(+), 107 deletions(-)

2011-06-06  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with invalid scroll range after deleting columns
 src/belvuApp/belvuAlignment.c | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

2011-05-31  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented functionality to remove columns to the left/right of the selected column
 src/belvuApp/belvuAlignment.c | 24 ++++++++++++++++++++++--
 src/belvuApp/belvuAlignment.h |  1 +
 src/belvuApp/belvuWindow.c    | 35 +++++++++++++++++++++++++++++++++++
 3 files changed, 58 insertions(+), 2 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Highlight all alignments with the same name as the currently-selected alignment
 src/belvuApp/belvuAlignment.c | 35 +++++++++++++++++++++++++++++------
 src/belvuApp/belvuWindow.c    |  2 +-
 2 files changed, 30 insertions(+), 7 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented middle-click scrolling
 src/belvuApp/belvuAlignment.c | 88 ++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 78 insertions(+), 10 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where clicking outside the sequence area was trying to select a column
 src/belvuApp/belvuAlignment.c | 36 ++++++++++++++++++++++++++++++++----
 1 file changed, 32 insertions(+), 4 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Highlight the selected column when middle-clicking
 src/belvuApp/belvu.c          |  2 ++
 src/belvuApp/belvuAlignment.c | 41 ++++++++++++++++++++++++++---------------
 src/belvuApp/belvuWindow.c    | 29 +++++++++++++++++++----------
 src/belvuApp/belvu_.h         | 10 +++++++---
 4 files changed, 54 insertions(+), 28 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying and renaming
 src/belvuApp/belvu.c          | 170 +++++++++++++++++++++---------------------
 src/belvuApp/belvuAlignment.c |  18 ++---
 src/belvuApp/belvuTree.c      |   4 +-
 src/belvuApp/belvuWindow.c    |  22 +++---
 src/belvuApp/belvu_.h         |   2 +-
 5 files changed, 108 insertions(+), 108 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying and renaming
 src/belvuApp/belvu.c          | 34 +++++++++++++++++-----------------
 src/belvuApp/belvuAlignment.c |  3 +--
 src/belvuApp/belvuWindow.c    | 12 ++++++------
 src/belvuApp/belvu_.h         |  2 +-
 4 files changed, 25 insertions(+), 26 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Feedback box is now updated when the selected row/column changes
 src/belvuApp/belvuWindow.c | 80 ++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 78 insertions(+), 2 deletions(-)

2011-05-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a compile error
 src/blixemApp/detailview.c | 16 ----------------
 1 file changed, 16 deletions(-)

2011-05-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a compile error
 src/belvuApp/belvuWindow.c | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2011-05-26  Gemma Barson  <gb10@sanger.ac.uk>
 Added feedback box to toolbar
 src/belvuApp/belvuAlignment.c |  2 +-
 src/belvuApp/belvuWindow.c    | 29 ++++++++++++++++++++++++++++-
 src/seqtoolsUtils/utilities.c | 16 ++++++++++++++++
 src/seqtoolsUtils/utilities.h |  1 +
 4 files changed, 46 insertions(+), 2 deletions(-)

2011-05-26  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to column-selection code
 src/belvuApp/belvuAlignment.c | 39 ++++++++++++++++++++++++++++-----------
 src/belvuApp/belvuTree.c      |  2 +-
 src/belvuApp/belvuWindow.c    | 13 ++++++++++++-
 src/belvuApp/belvuWindow.h    |  3 ++-
 4 files changed, 43 insertions(+), 14 deletions(-)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Added functionality to identify which row has been left-clicked
 src/belvuApp/belvu.c          |  1 +
 src/belvuApp/belvuAlignment.c | 25 +++++++++++++++++++++----
 src/belvuApp/belvu_.h         |  1 +
 3 files changed, 23 insertions(+), 4 deletions(-)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'remove columns' menu option
 src/belvuApp/belvu.c       | 21 ++++++++-------
 src/belvuApp/belvuWindow.c | 67 ++++++++++++++++++++++++++++++++++++++++++++++
 src/belvuApp/belvu_.h      |  1 +
 3 files changed, 80 insertions(+), 9 deletions(-)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Removed the default-sort menu option because it doesn't work correctly
 src/belvuApp/belvuWindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash where the tree becomes invalidated after deleting sequences
 src/belvuApp/belvuTree.c | 3 +++
 1 file changed, 3 insertions(+)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'exclude highlighted' menu option
 src/belvuApp/belvu.c          | 73 +++++++++++++++++++++++++------------------
 src/belvuApp/belvuAlignment.c |  2 +-
 src/belvuApp/belvuWindow.c    | 45 +++++++++++++++++++++-----
 src/belvuApp/belvu_.h         |  1 +
 4 files changed, 81 insertions(+), 40 deletions(-)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented greyscale colours for printing
 src/belvuApp/belvu.c          | 137 +++++++++++++++++++++++++++++++++++-------
 src/belvuApp/belvuAlignment.c |  41 +++++++++----
 src/belvuApp/belvuWindow.c    |  36 +++++++++--
 src/belvuApp/belvu_.h         |  30 ++++++---
 4 files changed, 198 insertions(+), 46 deletions(-)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'ignore gaps' option
 src/belvuApp/belvu.c       | 11 +++--------
 src/belvuApp/belvuWindow.c |  7 +++++++
 2 files changed, 10 insertions(+), 8 deletions(-)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression where the disable-colours option was broken
 src/belvuApp/belvuAlignment.c | 69 ++++++++++++++++++++++---------------------
 1 file changed, 35 insertions(+), 34 deletions(-)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Rearranged colour menus
 src/belvuApp/belvuWindow.c | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

2011-05-25  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented load/save of colour schemes
 src/belvuApp/belvu.c          | 100 ++++++++++++------------------------------
 src/belvuApp/belvuMain.c      |   9 +++-
 src/belvuApp/belvuWindow.c    |  30 ++++++++++++-
 src/belvuApp/belvu_.h         |   3 +-
 src/dotterApp/dotplot.c       |  70 +----------------------------
 src/seqtoolsUtils/utilities.c |  83 +++++++++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |   4 ++
 7 files changed, 153 insertions(+), 146 deletions(-)

2011-05-23  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying
 src/belvuApp/belvu.c       |  8 ++++++++
 src/belvuApp/belvuWindow.c | 46 ----------------------------------------------
 src/belvuApp/belvu_.h      |  1 +
 3 files changed, 9 insertions(+), 46 deletions(-)

2011-05-23  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with foreground colors in color-by-conservation mode
 src/belvuApp/belvuAlignment.c | 44 ++++++++++++++++++++++++++++++++-----------
 1 file changed, 33 insertions(+), 11 deletions(-)

2011-05-23  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented edit-conservation-colors dialog
 src/belvuApp/belvu.c           |  22 ++-
 src/belvuApp/belvuWindow.c     | 296 +++++++++++++++++++++++++++++++++++++----
 src/belvuApp/belvu_.h          |   2 +-
 src/doc/Design_notes/todo.html |   1 +
 4 files changed, 289 insertions(+), 32 deletions(-)

2011-05-23  Gemma Barson  <gb10@sanger.ac.uk>
 Added custom-color-scheme menu item
 src/belvuApp/belvu.c       | 121 +++++++++++++++++++++++++++++++++++++++++++--
 src/belvuApp/belvuMain.c   |   3 +-
 src/belvuApp/belvuWindow.c |  17 ++++---
 src/belvuApp/belvu_.h      |   3 ++
 4 files changed, 133 insertions(+), 11 deletions(-)

2011-05-23  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: Added 'custom' color scheme menu item for edited colors
 src/belvuApp/belvu.c       |   1 +
 src/belvuApp/belvuWindow.c | 138 +++++++++++++++++++++++++++++++++++++++------
 src/belvuApp/belvu_.h      |   6 +-
 3 files changed, 126 insertions(+), 19 deletions(-)

2011-05-18  Gemma Barson  <gb10@sanger.ac.uk>
 Added edit-residue-colors dialog
 src/belvuApp/belvu.c       |  20 +--
 src/belvuApp/belvuMain.c   |   2 +-
 src/belvuApp/belvuWindow.c | 372 ++++++++++++++++++++++++++++++++++++++++++---
 src/belvuApp/belvu_.h      |   4 +-
 4 files changed, 366 insertions(+), 32 deletions(-)

2011-05-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash when the tree settings are changed when there is no tree window
 src/belvuApp/belvuTree.c | 79 ++++++++++++++++++++++++++++++++++++------------
 1 file changed, 60 insertions(+), 19 deletions(-)

2011-05-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the tree distance calculations
 src/belvuApp/belvu.c          |  3 +-
 src/belvuApp/belvuTree.c      | 68 ++++++++++++++-----------------------------
 src/belvuApp/belvuTree.h      |  1 -
 src/belvuApp/belvuWindow.c    |  1 -
 src/seqtoolsUtils/utilities.c | 11 ++++---
 src/seqtoolsUtils/utilities.h |  9 ++++--
 6 files changed, 37 insertions(+), 56 deletions(-)

2011-05-17  Gemma Barson  <gb10@sanger.ac.uk>
 Added 'recalculate tree' menu option
 src/belvuApp/belvu.c       |  5 ++-
 src/belvuApp/belvuMain.c   |  2 +-
 src/belvuApp/belvuTree.c   | 50 +++++++++++++++++-------
 src/belvuApp/belvuTree.h   |  8 +++-
 src/belvuApp/belvuWindow.c | 95 +++++++++++++++++++++++++++++++++++-----------
 src/belvuApp/belvu_.h      |  8 ++--
 6 files changed, 124 insertions(+), 44 deletions(-)

2011-05-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where tree-sort was getting messed up after changing tree order
 src/belvuApp/belvu.c       | 14 +++++++-------
 src/belvuApp/belvuWindow.c |  9 ++++++++-
 2 files changed, 15 insertions(+), 8 deletions(-)

2011-05-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the tree drawing area size was not recalculated when on re-root
 src/belvuApp/belvuTree.c | 5 +++++
 1 file changed, 5 insertions(+)

2011-05-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the tree was not being updated when re-rooting
 src/belvuApp/belvuTree.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2011-05-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with sorting
 src/belvuApp/belvu.c | 38 ++++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 18 deletions(-)

2011-05-16  Gemma Barson  <gb10@sanger.ac.uk>
 Alignment sort order is now updated when tree order has changed
 src/belvuApp/belvu.c       | 162 +++++++++++++++++++++++++--------------------
 src/belvuApp/belvuMain.c   |  18 +++--
 src/belvuApp/belvuTree.c   |  80 +++++++++++++---------
 src/belvuApp/belvuWindow.c |  15 ++++-
 src/belvuApp/belvu_.h      |  29 ++++----
 5 files changed, 176 insertions(+), 128 deletions(-)

2011-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Only allow one tree
 src/belvuApp/belvu.c       |   5 +-
 src/belvuApp/belvuTree.c   | 177 ++++++++++++++++++++++++++++++++-------------
 src/belvuApp/belvuTree.h   |   2 +-
 src/belvuApp/belvuWindow.c |  88 ++++++----------------
 src/belvuApp/belvu_.h      |   2 +-
 5 files changed, 157 insertions(+), 117 deletions(-)

2011-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented tree-swap and tree-reroot
 src/belvuApp/belvu.c          |  11 ----
 src/belvuApp/belvuAlignment.c |  20 +++---
 src/belvuApp/belvuTree.c      | 142 ++++++++++++++++++++++--------------------
 src/belvuApp/belvuWindow.c    |   6 ++
 src/belvuApp/belvuWindow.h    |   1 +
 5 files changed, 89 insertions(+), 91 deletions(-)

2011-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Alignment display now re-centres when selecting alignments in a tree
 src/belvuApp/belvuAlignment.c | 15 +++++++++++++--
 src/belvuApp/belvuWindow.c    |  2 ++
 2 files changed, 15 insertions(+), 2 deletions(-)

2011-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented the 'clean up windows' option
 src/belvuApp/belvuWindow.c | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

2011-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Added notes about a historic Belvu bug
 src/doc/Design_notes/todo.html | 1 +
 1 file changed, 1 insertion(+)

2011-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Trees are now updated dynamically when the selection changes
 src/belvuApp/belvu.c          | 11 ++++--
 src/belvuApp/belvuAlignment.c |  9 +++--
 src/belvuApp/belvuMain.c      | 10 +++---
 src/belvuApp/belvuTree.c      | 36 ++++++++++++++-----
 src/belvuApp/belvuTree.h      |  7 ++--
 src/belvuApp/belvuWindow.c    | 82 ++++++++++++++++++++++++++-----------------
 src/belvuApp/belvuWindow.h    |  2 +-
 src/belvuApp/belvu_.h         | 12 ++++---
 8 files changed, 106 insertions(+), 63 deletions(-)

2011-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Selected sequences are now highlighted in trees
 src/belvuApp/belvu.c          |  6 +++++-
 src/belvuApp/belvuAlignment.c | 29 +++++++++++++----------------
 src/belvuApp/belvuTree.c      | 41 +++++++++++++++++++++++++----------------
 src/belvuApp/belvuWindow.c    |  6 +++++-
 src/belvuApp/belvu_.h         |  8 +++++---
 5 files changed, 53 insertions(+), 37 deletions(-)

2011-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Clicking on a tree node now selects that alignment
 src/belvuApp/belvu.c       |  2 ++
 src/belvuApp/belvuTree.c   | 10 +++++-----
 src/belvuApp/belvuWindow.c | 22 +++++++++++++++++++---
 src/belvuApp/belvuWindow.h |  2 ++
 src/belvuApp/belvu_.h      |  2 ++
 5 files changed, 30 insertions(+), 8 deletions(-)

2011-05-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug when coloring by residue ID
 src/belvuApp/belvu.c          | 24 +++++++++++++++++++-----
 src/belvuApp/belvuAlignment.c |  2 +-
 src/belvuApp/belvu_.h         |  2 ++
 3 files changed, 22 insertions(+), 6 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the colors were not correctly updated when changing color scheme with color-by-res-id is enabled
 src/belvuApp/belvu.c | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Added separate menu item to set threshold for color-by-res-id option
 src/belvuApp/belvuWindow.c | 32 +++++++++++++++++++++++---------
 1 file changed, 23 insertions(+), 9 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented color-by-res-id option
 src/belvuApp/belvu.c       | 21 +++++------------
 src/belvuApp/belvuWindow.c | 58 +++++++++++++++++++++++++++++++++++++++++-----
 2 files changed, 58 insertions(+), 21 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented highlight-lowercase-characters option
 src/belvuApp/belvuWindow.c | 5 +++++
 src/belvuApp/belvu_.h      | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented toggle-color-scheme option
 src/belvuApp/belvu.c       |  2 +-
 src/belvuApp/belvuWindow.c | 64 +++++++++++++++++++++++++++++++---------------
 src/belvuApp/belvu_.h      |  2 +-
 3 files changed, 45 insertions(+), 23 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented color by residue color schemes
 src/belvuApp/belvuWindow.c | 13 +++++++++++--
 src/belvuApp/belvu_.h      |  1 +
 2 files changed, 12 insertions(+), 2 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented conservation color schemes
 src/belvuApp/belvu.c          | 957 ++++++++++++++++++++++--------------------
 src/belvuApp/belvuAlignment.c |   6 +-
 src/belvuApp/belvuMain.c      |  14 +-
 src/belvuApp/belvuWindow.c    |  69 ++-
 src/belvuApp/belvu_.h         |  23 +-
 5 files changed, 581 insertions(+), 488 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented toggle-display-colors option
 src/belvuApp/belvu.c          |  2 ++
 src/belvuApp/belvuAlignment.c | 27 +++++++++++++++------------
 src/belvuApp/belvuMain.c      |  7 +++----
 src/belvuApp/belvuWindow.c    | 16 +++++++++++-----
 src/belvuApp/belvu_.h         |  1 +
 5 files changed, 32 insertions(+), 21 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Added ability to sort by conservation order
 src/belvuApp/belvu.c       | 5 +++--
 src/belvuApp/belvuWindow.c | 4 +++-
 src/belvuApp/belvu_.h      | 1 +
 3 files changed, 7 insertions(+), 3 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented sort-by menu options
 src/belvuApp/belvu.c       | 2443 +++++++++++++++++++++++---------------------
 src/belvuApp/belvuMain.c   |   44 +-
 src/belvuApp/belvuWindow.c |    8 +
 src/belvuApp/belvu_.h      |    1 +
 4 files changed, 1279 insertions(+), 1217 deletions(-)

2011-05-12  Gemma Barson  <gb10@sanger.ac.uk>
 Tidied the sort-by enums
 src/belvuApp/belvuMain.c | 51 ++++++++++++++++++++++++++----------------------
 src/belvuApp/belvu_.h    |  4 ++--
 2 files changed, 30 insertions(+), 25 deletions(-)

2011-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: added ability to select a node from the tree window
 src/belvuApp/belvuTree.c | 92 ++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 89 insertions(+), 3 deletions(-)

2011-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Tree window now has a scale
 src/belvuApp/belvuTree.c | 123 ++++++++++++++++++++++++++++-------------------
 1 file changed, 74 insertions(+), 49 deletions(-)

2011-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Tree layout size is now more accurate
 src/belvuApp/belvu.c          | 20 ++++++++--
 src/belvuApp/belvuAlignment.c | 20 +++++-----
 src/belvuApp/belvuTree.c      | 85 ++++++++++++++++++++++++++++++-------------
 src/belvuApp/belvu_.h         |  4 +-
 4 files changed, 88 insertions(+), 41 deletions(-)

2011-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Set the make-tree dialog's focus on a widget that can activate the default response
 src/belvuApp/belvuTree.c   | 16 +++++++++-------
 src/belvuApp/belvuTree.h   |  2 +-
 src/belvuApp/belvuWindow.c | 13 +++++++++----
 3 files changed, 19 insertions(+), 12 deletions(-)

2011-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Added ability to set the tree building method via the make-tree dialog
 src/belvuApp/belvuTree.c   | 14 ++++++--------
 src/belvuApp/belvuWindow.c | 47 ++++++++++++++++++++++++++++++++++++++++++++--
 src/belvuApp/belvu_.h      |  6 ++++++
 3 files changed, 57 insertions(+), 10 deletions(-)

2011-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Generalised combo box functions
 src/belvuApp/belvuTree.c      | 64 +---------------------------------------
 src/belvuApp/belvu_.h         | 10 -------
 src/seqtoolsUtils/utilities.c | 68 ++++++++++++++++++++++++++++++++++++++++++-
 src/seqtoolsUtils/utilities.h | 17 +++++++++++
 4 files changed, 85 insertions(+), 74 deletions(-)

2011-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Added ability to choose the pick method on the tree settings dialog
 src/belvuApp/belvu.c       |   1 +
 src/belvuApp/belvuMain.c   |   1 -
 src/belvuApp/belvuTree.c   | 111 ++++++++++++++++++++++++++++++++++++++++-----
 src/belvuApp/belvuTree.h   |   6 ++-
 src/belvuApp/belvuWindow.c |   5 +-
 src/belvuApp/belvu_.h      |  32 +++++++++----
 6 files changed, 134 insertions(+), 22 deletions(-)

2011-05-11  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some uninitialised-value warnings
 src/belvuApp/belvu.c     | 144 +++++++++++++++++++++++++++++------------------
 src/belvuApp/belvuMain.c |  13 +++--
 src/belvuApp/belvuTree.c |  67 +++++++++++-----------
 src/belvuApp/belvu_.h    |   6 +-
 4 files changed, 132 insertions(+), 98 deletions(-)

2011-05-10  Gemma Barson  <gb10@sanger.ac.uk>
 Added ability to change the line width and tree scale
 src/belvuApp/belvuTree.c   | 91 +++++++++++++++++++++++++++++++++++++++-------
 src/belvuApp/belvuTree.h   |  2 +-
 src/belvuApp/belvuWindow.c |  2 +-
 3 files changed, 79 insertions(+), 16 deletions(-)

2011-05-10  Gemma Barson  <gb10@sanger.ac.uk>
 Tree settings dialog now refreshes the tree
 src/belvuApp/belvuTree.c | 51 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 50 insertions(+), 1 deletion(-)

2011-05-10  Gemma Barson  <gb10@sanger.ac.uk>
 Added comments
 src/seqtoolsUtils/utilities.c | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

2011-05-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a memory bug where the tree settings dialog response function was being passed invalid data
 src/belvuApp/belvuTree.c | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

2011-05-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with branch length text position
 src/belvuApp/belvuTree.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-05-10  Gemma Barson  <gb10@sanger.ac.uk>
 Code tidying
 src/belvuApp/belvuTree.c | 166 ++++++++++++++++++++++++++++++-----------------
 1 file changed, 108 insertions(+), 58 deletions(-)

2011-05-10  Gemma Barson  <gb10@sanger.ac.uk>
 Added make-tree and tree-settings dialogs
 src/belvuApp/belvu.c       |   3 +-
 src/belvuApp/belvuTree.c   | 180 +++++++++++++++++++++++++++++++++------------
 src/belvuApp/belvuTree.h   |   4 +-
 src/belvuApp/belvuWindow.c | 103 +++++++++++++++++++++++---
 src/belvuApp/belvu_.h      |  53 ++++++++++---
 5 files changed, 277 insertions(+), 66 deletions(-)

2011-05-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where scores were being displayed incorrectly
 src/belvuApp/belvu.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-05-06  Gemma Barson  <gb10@sanger.ac.uk>
 The tree now draws correct sequence names and has thicker lines
 src/belvuApp/belvuTree.c | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

2011-05-06  Gemma Barson  <gb10@sanger.ac.uk>
 Added basic tree drawing capability
 src/belvuApp/belvu.c          | 262 +++++++++++++++---------------------------
 src/belvuApp/belvuAlignment.c |  68 -----------
 src/belvuApp/belvuMain.c      |  30 +++--
 src/belvuApp/belvuTree.c      | 217 ++++++++++++++++++++++++++++++----
 src/belvuApp/belvuWindow.c    |   2 +
 src/belvuApp/belvu_.h         |  13 ++-
 6 files changed, 318 insertions(+), 274 deletions(-)

2011-05-06  Gemma Barson  <gb10@sanger.ac.uk>
 Windows now have proper titles
 src/belvuApp/belvuTree.c   | 19 ++++++++++---------
 src/belvuApp/belvuWindow.c | 13 +++++++++++--
 2 files changed, 21 insertions(+), 11 deletions(-)

2011-05-06  Gemma Barson  <gb10@sanger.ac.uk>
 Added tree-drawing widgets
 src/belvuApp/Makefile.am      |    2 +-
 src/belvuApp/belvu.c          | 1189 ++-------------------------------
 src/belvuApp/belvuAlignment.c |   23 +-
 src/belvuApp/belvuAlignment.h |    2 +-
 src/belvuApp/belvuMain.c      |    3 +-
 src/belvuApp/belvuTree.c      | 1473 +++++++++++++++++++++++++++++++++++++++++
 src/belvuApp/belvuTree.h      |   54 ++
 src/belvuApp/belvuWindow.c    |   43 +-
 src/belvuApp/belvuWindow.h    |    5 +-
 src/belvuApp/belvu_.h         |   10 +-
 src/seqtoolsUtils/utilities.c |   24 +-
 src/seqtoolsUtils/utilities.h |    1 +
 12 files changed, 1637 insertions(+), 1192 deletions(-)

2011-05-05  Gemma Barson  <gb10@sanger.ac.uk>
 Added remove-by-score and remove-outliers
 src/belvuApp/belvu.c          | 290 +++++++++++++++++++++---------------------
 src/belvuApp/belvuAlignment.c |  30 +++++
 src/belvuApp/belvuAlignment.h |   5 +
 src/belvuApp/belvuWindow.c    |  57 +++++++++
 src/belvuApp/belvu_.h         |   2 +
 5 files changed, 241 insertions(+), 143 deletions(-)

2011-05-05  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented remove-partial and make-non-redundant
 src/belvuApp/belvu.c          | 43 ++++++--------------
 src/belvuApp/belvuAlignment.c | 17 +++++++-
 src/belvuApp/belvuAlignment.h |  4 +-
 src/belvuApp/belvuMain.c      |  2 +-
 src/belvuApp/belvuWindow.c    | 93 ++++++++++++++++++++++++++++++++-----------
 src/belvuApp/belvu_.h         |  2 +-
 6 files changed, 102 insertions(+), 59 deletions(-)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'remove gappy sequences' option
 src/belvuApp/belvu.c          |  9 ++++--
 src/belvuApp/belvuAlignment.c | 11 ++++++-
 src/belvuApp/belvuAlignment.h |  2 +-
 src/belvuApp/belvuWindow.c    | 71 ++++++++++++++++++++++++++++++++++++++++---
 4 files changed, 84 insertions(+), 9 deletions(-)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Removed padding around alignment view
 src/belvuApp/belvuAlignment.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'remove sequences' mode
 src/belvuApp/belvuAlignment.c | 36 ++++++++++++++++++++++++++++++++++--
 src/belvuApp/belvuAlignment.h |  1 +
 src/belvuApp/belvuWindow.c    | 42 +++++++++++++++++++-----------------------
 3 files changed, 54 insertions(+), 25 deletions(-)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added flag and cursor for 'remove sequences' mode
 src/belvuApp/belvuWindow.c | 78 +++++++++++++++++++++++++++++++++++++++++-----
 src/belvuApp/belvu_.h      |  1 +
 2 files changed, 71 insertions(+), 8 deletions(-)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added help menu
 src/belvuApp/belvuWindow.c | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added About dialog
 src/belvuApp/belvuWindow.c | 64 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Update vertical scroll range when deleting rows
 src/belvuApp/belvuAlignment.c | 37 ++++++++++++++++++++++++++++++-------
 src/belvuApp/belvuAlignment.h |  3 ++-
 src/belvuApp/belvuWindow.c    | 21 ++++++++++++++-------
 3 files changed, 46 insertions(+), 15 deletions(-)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the last base was not visible
 src/belvuApp/belvuAlignment.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Selected row is now highlighted
 src/belvuApp/belvuAlignment.c | 26 ++++++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Implemented 'remove row' option
 src/belvuApp/belvuWindow.c | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

2011-04-21  Gemma Barson  <gb10@sanger.ac.uk>
 Select a row when it is clicked
 src/belvuApp/belvuAlignment.c | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added toggle and radio menu actions
 src/belvuApp/belvuWindow.c | 214 +++++++++++++++++++++------------------------
 src/belvuApp/belvu_.h      |  42 ++++++++-
 2 files changed, 140 insertions(+), 116 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Moved long menus to sub-menus
 src/belvuApp/belvuWindow.c | 46 +++++++++++++++++++++++++++-------------------
 1 file changed, 27 insertions(+), 19 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added Edit, Color and Sort menu actions
 src/belvuApp/belvuWindow.c | 383 +++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 374 insertions(+), 9 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where closing the wrap window was quitting the application
 src/belvuApp/belvuAlignment.c | 2 --
 1 file changed, 2 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Set initial position of wrap window
 src/belvuApp/belvuWindow.c | 43 +++++++++++++++++++++++++++++--------------
 1 file changed, 29 insertions(+), 14 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Use more sensible window sizes, and bring wrap window to front on creation
 src/belvuApp/belvuWindow.c | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with printing a non-toplevel widget
 src/belvuApp/belvuWindow.c    | 4 ++--
 src/blixemApp/blxwindow.c     | 2 +-
 src/dotterApp/alignmenttool.c | 2 +-
 src/dotterApp/dotter.c        | 4 ++--
 src/seqtoolsUtils/utilities.c | 3 ++-
 src/seqtoolsUtils/utilities.h | 2 +-
 6 files changed, 9 insertions(+), 8 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added title to wrapped-alignment view
 src/belvuApp/belvuAlignment.c | 30 ++++++++++++++++++++++++++----
 src/belvuApp/belvuAlignment.h |  2 +-
 src/belvuApp/belvuWindow.c    |  8 ++------
 3 files changed, 29 insertions(+), 11 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a scaling issue with printing fit-to-width
 src/seqtoolsUtils/utilities.c | 24 ++++++++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added printing for the wrapped-alignment view
 src/belvuApp/belvuWindow.c    |  76 +++++++++++++++-----
 src/blixemApp/blxwindow.c     |   2 +-
 src/dotterApp/alignmenttool.c |   2 +-
 src/dotterApp/dotter.c        |   4 +-
 src/seqtoolsUtils/utilities.c | 158 +++++++++++++++++++++++++++++++++---------
 src/seqtoolsUtils/utilities.h |  12 +++-
 6 files changed, 202 insertions(+), 52 deletions(-)

2011-04-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with the wrapped view
 src/belvuApp/belvuAlignment.c | 152 ++++++++++++++++++++++++++----------------
 1 file changed, 96 insertions(+), 56 deletions(-)

2011-04-19  Gemma Barson  <gb10@sanger.ac.uk>
 Added wrapped-alignment view
 src/belvuApp/belvu.c          |  19 +--
 src/belvuApp/belvuAlignment.c | 355 +++++++++++++++++++++++++++++++++++++-----
 src/belvuApp/belvuAlignment.h |   2 +-
 src/belvuApp/belvuWindow.c    | 260 ++++++++++++++++++++++++++++---
 src/belvuApp/belvu_.h         |   1 +
 5 files changed, 559 insertions(+), 78 deletions(-)

2011-04-19  Gemma Barson  <gb10@sanger.ac.uk>
 Improved start up speed
 src/belvuApp/belvuAlignment.c | 164 ++++++++++++++++++++++++++----------------
 1 file changed, 104 insertions(+), 60 deletions(-)

2011-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Added column separater lines
 src/belvuApp/belvuAlignment.c | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

2011-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue with aligning the columns
 src/belvuApp/belvuAlignment.c | 32 ++++++++++++++------------------
 1 file changed, 14 insertions(+), 18 deletions(-)

2011-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Removed unnecessary calls to size-allocate
 src/belvuApp/belvuAlignment.c | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

2011-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 The horizontal scrollbar now only affects the sequence column
 src/belvuApp/belvuAlignment.c | 257 ++++++++++++++++++++++++++++--------------
 1 file changed, 174 insertions(+), 83 deletions(-)

2011-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Cached the drawable for the belvu alignment
 src/belvuApp/belvuAlignment.c | 56 +++++++++++++++++++++++++------------------
 1 file changed, 33 insertions(+), 23 deletions(-)

2011-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 WIP belvu now uses fixed-width font
 src/belvuApp/belvuAlignment.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2011-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: belvu now shows colors
 src/belvuApp/belvu.c          | 57 +++++++++++++++++--------
 src/belvuApp/belvuAlignment.c | 99 ++++++++++++++++++++++++++++++++++++++-----
 src/belvuApp/belvuMain.c      | 54 ++---------------------
 src/belvuApp/belvu_.h         | 11 +++++
 src/seqtoolsUtils/utilities.h | 10 +++++
 5 files changed, 153 insertions(+), 78 deletions(-)

2011-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: create belvu main window
 src/belvuApp/Makefile.am                |   2 +-
 src/belvuApp/belvu.c                    | 110 +++++++++++
 src/belvuApp/belvuAlignment.c           | 301 +++++++++++++++++++++++++++++
 src/belvuApp/belvuAlignment.h           |  48 +++++
 src/belvuApp/belvuMain.c                | 232 ++++++++---------------
 src/belvuApp/belvuWindow.c              | 326 +++++++++++++++++++++++++++++++-
 src/belvuApp/belvuWindow.h              |   2 +-
 src/belvuApp/belvu_.h                   |  19 ++
 src/doc/User_doc/Makefile.am            |   6 +-
 src/doc/User_doc/belvu_news.html        |   9 +
 src/doc/User_doc/belvu_quick_start.html |  65 +++++++
 src/doc/User_doc/belvu_usage.txt        |  75 ++++++++
 src/doc/User_doc/index.html             |   7 +
 13 files changed, 1039 insertions(+), 163 deletions(-)

2011-04-11  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: added belvu files
 .gitignore                 |    1 +
 src/Makefile.am            |    7 +-
 src/belvuApp/Makefile.am   |    8 +
 src/belvuApp/belvu.c       | 8524 ++++++++++++++++++++++++++++++++++++++++++++
 src/belvuApp/belvuMain.c   |  876 +++++
 src/belvuApp/belvuOld.c    | 8386 +++++++++++++++++++++++++++++++++++++++++++
 src/belvuApp/belvuWindow.c |   95 +
 src/belvuApp/belvuWindow.h |   48 +
 src/belvuApp/belvu_.h      |  339 ++
 src/configure.ac           |    2 +-
 10 files changed, 18283 insertions(+), 3 deletions(-)

2011-04-08  Gemma Barson  <gb10@sanger.ac.uk>
 Edited comments
 src/seqtoolsUtils/blxparser.c | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

2011-04-08  Gemma Barson  <gb10@sanger.ac.uk>
 Generalised FASTA parser to allow multiple sequences
 src/blixemApp/blxmain.c       |  73 +----------------
 src/seqtoolsUtils/blxparser.c | 183 ++++++++++++++++++++++++++----------------
 2 files changed, 117 insertions(+), 139 deletions(-)

2011-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression with the default zoom range
 src/blixemApp/bigpicture.c | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2011-07-13  Gemma Barson  <gb10@sanger.ac.uk>
 Added 'read' type
 src/seqtoolsUtils/blxGff3Parser.c | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

2011-07-12  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some issues where scrolling messes up the initial big picture range
 src/blixemApp/bigpicture.c |  5 +++--
 src/blixemApp/detailview.c | 11 ++++++++---
 2 files changed, 11 insertions(+), 5 deletions(-)

2011-07-11  Gemma Barson  <gb10@sanger.ac.uk>
 Added --zoom-range argument to allow the caller to specify the initial big picture range
 src/blixemApp/bigpicture.c | 45 +++++++++--------------------
 src/blixemApp/bigpicture.h |  2 ++
 src/blixemApp/blixem_.h    |  2 ++
 src/blixemApp/blxmain.c    | 72 +++++++++++++++++++++++++++++++++-------------
 src/blixemApp/blxwindow.c  | 12 +++++++-
 5 files changed, 81 insertions(+), 52 deletions(-)

2011-07-04  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed typos where a gboolean was being used instead of an int
 src/blixemApp/blixem_.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-06-17  Gemma Barson  <gb10@sanger.ac.uk>
 Updated blixem user manual with info about the coverage view
 src/doc/User_doc/Blixem_manual.odt | Bin 1095666 -> 1102821 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 849234 -> 855666 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-06-17  Gemma Barson  <gb10@sanger.ac.uk>
 Updated what's new page
 src/doc/User_doc/blixem_news.html | 7 +++++++
 1 file changed, 7 insertions(+)

2011-06-17  Gemma Barson  <gb10@sanger.ac.uk>
 Ensure that only identical alignments can appear on the same row in 'squash matches' mode
 src/blixemApp/detailviewtree.c | 40 ++++++++++++++++++++++++++++++++--------
 1 file changed, 32 insertions(+), 8 deletions(-)

2011-06-17  Gemma Barson  <gb10@sanger.ac.uk>
 Do not show score and ID if they are unset
 src/blixemApp/detailviewtree.c | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

2011-06-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where some short reads were not being added to the 'squashed' view
 src/blixemApp/detailviewtree.c | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

2011-06-15  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/shortread'
2011-06-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where dotter fails if pfetch returns 'no match'
 src/blixemApp/blxdotter.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-06-15  Gemma Barson  <gb10@sanger.ac.uk>
 When sorting alignments by position, also do a secondary sort by length
 src/blixemApp/detailviewtree.c | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

2011-06-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where the 'squash matches' option on the settings dialog was not updated after changing the same setting on the toolbar
 src/blixemApp/blxwindow.c     | 21 ++++++++++++++++-----
 src/seqtoolsUtils/utilities.c | 38 ++++++++++++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |  3 +++
 3 files changed, 57 insertions(+), 5 deletions(-)

2011-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.2 (start of new versioning system)
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/shortread'
2011-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to message handling for region-fetch code
 src/blixemApp/blxview.c       | 22 ++++++++++++++--------
 src/blixemApp/blxwindow.c     |  2 +-
 src/seqtoolsUtils/utilities.c | 25 +++++++++++++++++++++++--
 src/seqtoolsUtils/utilities.h |  1 +
 4 files changed, 39 insertions(+), 11 deletions(-)

2011-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue with squashed matches where the row was not always highlighted correctly for selected/grouped matches
 src/blixemApp/blxwindow.c            |  3 +++
 src/blixemApp/sequencecellrenderer.c | 46 ++++++++++++++++++++++++++++++++----
 src/seqtoolsUtils/utilities.c        | 12 +++++-----
 src/seqtoolsUtils/utilities.h        |  8 +++----
 4 files changed, 55 insertions(+), 14 deletions(-)

2011-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Small comment addition
 src/dotterApp/dotter.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Added toolbar icon for squash-matches option
 src/blixemApp/blxwindow.c | 33 +++++++++++++++++++++++++++++----
 1 file changed, 29 insertions(+), 4 deletions(-)

2011-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Improved display name for short reads when 'squash matches' is enabled
 src/blixemApp/detailview.h     |  3 ++-
 src/blixemApp/detailviewtree.c | 17 +++++++----------
 2 files changed, 9 insertions(+), 11 deletions(-)

2011-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where a selected short-read could be hidden by its duplicates in 'squashed matches' mode
 src/blixemApp/sequencecellrenderer.c | 35 +++++++++++++++++++++++++++++------
 1 file changed, 29 insertions(+), 6 deletions(-)

2011-06-14  Gemma Barson  <gb10@sanger.ac.uk>
 Finished work to group short-reads
 src/blixemApp/detailviewtree.c | 186 ++++++++++++++++++++++++++++++++---------
 src/seqtoolsUtils/blxmsp.c     |   2 +-
 2 files changed, 149 insertions(+), 39 deletions(-)

2011-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: implement a better way of grouping duplicate short reads
 src/blixemApp/detailviewtree.c    |  3 +-
 src/seqtoolsUtils/blxGff3Parser.c |  2 +-
 src/seqtoolsUtils/blxmsp.c        | 67 ++-------------------------------------
 src/seqtoolsUtils/blxmsp.h        |  2 +-
 4 files changed, 7 insertions(+), 67 deletions(-)

2011-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue with the names of duplicated short reads being lost
 src/blixemApp/blxwindow.c      | 40 ++++-----------------------
 src/blixemApp/detailview.c     |  8 ++----
 src/blixemApp/detailview.h     |  6 ++++
 src/blixemApp/detailviewtree.c | 21 ++++----------
 src/seqtoolsUtils/blxmsp.c     | 63 ++++--------------------------------------
 src/seqtoolsUtils/blxmsp.h     |  6 ++--
 src/seqtoolsUtils/utilities.c  | 17 ------------
 src/seqtoolsUtils/utilities.h  |  1 -
 8 files changed, 28 insertions(+), 134 deletions(-)

2011-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the region-fetch script args were not being picked up from config
 src/blixemApp/blixem_.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a compile error on Macs (missing include file)
 src/blixemApp/blxview.c | 19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

2011-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a compile error on Linux due to missing include file
 src/blixemApp/blxview.c | 1 +
 1 file changed, 1 insertion(+)

2011-06-13  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/shortread'
2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the coverage view labels were sometimes not drawn correctly
 src/blixemApp/coverageview.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Added squash-matches command-line argument
 src/blixemApp/blixem_.h        |  2 +-
 src/blixemApp/blxmain.c        | 37 +++++++++++++++++++++++--------------
 src/blixemApp/blxwindow.c      | 17 +++++++++++++----
 src/blixemApp/detailviewtree.c |  2 +-
 4 files changed, 38 insertions(+), 20 deletions(-)

2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 By default, set the secondary sort column to be position
 src/blixemApp/detailview.c | 6 ++++++
 1 file changed, 6 insertions(+)

2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Added show-coverage command-line argument
 src/blixemApp/blixem_.h   | 2 ++
 src/blixemApp/blxmain.c   | 6 ++++++
 src/blixemApp/blxwindow.c | 7 ++++---
 3 files changed, 12 insertions(+), 3 deletions(-)

2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Report an error if the region-fetch script fails
 src/blixemApp/blxview.c | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 The range requested by region-fetch is now clipped to the display range
 src/blixemApp/blixem_.h   |  1 +
 src/blixemApp/blxview.c   | 32 +++++++++++++++++++++++---------
 src/blixemApp/blxwindow.c |  2 +-
 3 files changed, 25 insertions(+), 10 deletions(-)

2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Tidied the regino-fetch code
 src/blixemApp/blxview.c | 218 +++++++++++++++++++++++++++++++-----------------
 1 file changed, 143 insertions(+), 75 deletions(-)

2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Added the --save-temp-files command-line argument
 src/blixemApp/blixem_.h   |  3 +++
 src/blixemApp/blxmain.c   |  7 ++++++-
 src/blixemApp/blxview.c   | 19 ++++++++++++++-----
 src/blixemApp/blxwindow.c |  7 ++++---
 4 files changed, 27 insertions(+), 9 deletions(-)

2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 Keep original name for short reads so that we can identify pairs (until we have a better method of doing so)
 src/blixemApp/detailviewtree.c |  9 ++++-----
 src/seqtoolsUtils/blxmsp.c     | 13 +++++++------
 2 files changed, 11 insertions(+), 11 deletions(-)

2011-06-10  Gemma Barson  <gb10@sanger.ac.uk>
 GFF parser now ignores features that are outside the reference sequence range
 src/blixemApp/blxmain.c           |  7 +++++++
 src/seqtoolsUtils/blxGff3Parser.c | 33 +++++++++++++++++++++++++++------
 src/seqtoolsUtils/blxGff3Parser.h |  3 ++-
 src/seqtoolsUtils/blxparser.c     |  7 ++++---
 4 files changed, 40 insertions(+), 10 deletions(-)

2011-06-07  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/shortread'
2011-06-07  Gemma Barson  <gb10@sanger.ac.uk>
 Delete temp files after doing a region-fetch
 src/blixemApp/blxview.c | 5 +++++
 1 file changed, 5 insertions(+)

2011-06-07  Gemma Barson  <gb10@sanger.ac.uk>
 region-fetch now gets its script arguments from the config file on a per-source basis
 src/blixemApp/blxview.c | 161 ++++++++++++++++++++++++++----------------------
 1 file changed, 86 insertions(+), 75 deletions(-)

2011-06-03  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/buildsys'
2011-06-03  Gemma Barson  <gb10@sanger.ac.uk>
 Removed --dirty option from git describe because it's not available in older versions of git
 src/configure.ac | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

2011-06-03  Gemma Barson  <gb10@sanger.ac.uk>
 Use abbreviated commit ids in build info
 src/configure.ac | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-06-03  Gemma Barson  <gb10@sanger.ac.uk>
 Removed unused expression in configure.ac
 src/configure.ac | 2 --
 1 file changed, 2 deletions(-)

2011-06-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug in the build system where AM_COND_IF is not recognised in older versions of automake
 src/configure.ac | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

2011-06-03  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'feature/buildsys'
2011-06-03  Gemma Barson  <gb10@sanger.ac.uk>
 Build system now includes git-describe info in the version number
 src/blixemApp/blixem_.h | 4 ++--
 src/configure.ac        | 6 ++++++
 src/dotterApp/dotter_.h | 4 ++--
 3 files changed, 10 insertions(+), 4 deletions(-)

2011-06-02  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.20
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-06-02  Gemma Barson  <gb10@sanger.ac.uk>
 Added --dataset argument
 src/blixemApp/blixem_.h   |  5 ++++-
 src/blixemApp/blxmain.c   |  6 ++++++
 src/blixemApp/blxview.c   | 21 +++++++++++++++------
 src/blixemApp/blxwindow.c |  3 ++-
 4 files changed, 27 insertions(+), 8 deletions(-)

2011-06-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with creating temp files for region-fetch
 src/blixemApp/blxview.c | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

2011-06-01  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'shortread'
2011-05-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the parser was not ignoring blank lines
 src/seqtoolsUtils/blxparser.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-05-31  Gemma Barson  <gb10@sanger.ac.uk>
 Added the real script arguments for the bam-fetch script
 src/blixemApp/blxview.c           | 115 +++++++++++++++++++++-----------------
 src/blixemApp/blxwindow.c         |   2 +-
 src/seqtoolsUtils/blxGff3Parser.c |  18 +++---
 3 files changed, 73 insertions(+), 62 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Added code to distinguish short-read matches from other match types
 src/seqtoolsUtils/blxGff3Parser.c | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where parsing a secondary input file was not adding the sequences correctly
 src/blixemApp/blixem_.h |  2 +-
 src/blixemApp/blxview.c | 22 +++++++++++-----------
 2 files changed, 12 insertions(+), 12 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem region-fetch now calls the script specified in the config file
 src/blixemApp/blxview.c | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

2011-05-27  Gemma Barson  <gb10@sanger.ac.uk>
 Convert coords to chromosome (input) coords for bam-fetch
 src/blixemApp/blixem_.h   |  8 +++++---
 src/blixemApp/blxmain.c   |  1 -
 src/blixemApp/blxview.c   | 18 +++++++++++++-----
 src/blixemApp/blxwindow.c |  8 ++++++--
 4 files changed, 24 insertions(+), 11 deletions(-)

2011-05-05  Gemma Barson  <gb10@sanger.ac.uk>
 Region-fetch now parses the results of the created file
 src/blixemApp/blixem_.h    | 12 +++++++-
 src/blixemApp/blxmain.c    |  3 --
 src/blixemApp/blxview.c    | 74 ++++++++++++++++++++++++++++++++++++++++++----
 src/blixemApp/blxwindow.c  |  2 +-
 src/seqtoolsUtils/blxmsp.c |  6 ++++
 src/seqtoolsUtils/blxmsp.h |  1 +
 6 files changed, 87 insertions(+), 11 deletions(-)

2011-05-05  Gemma Barson  <gb10@sanger.ac.uk>
 Write some test data to the output file
 src/blixemApp/blxview.c    | 62 +++++++++++++++++++++++++++++++++++-----------
 src/seqtoolsUtils/blxmsp.c |  5 ++--
 2 files changed, 51 insertions(+), 16 deletions(-)

2011-05-05  Gemma Barson  <gb10@sanger.ac.uk>
 Region-fetch function now opens a temporary file for the results
 src/blixemApp/blxview.c | 35 ++++++++++++++++++++++++-----------
 1 file changed, 24 insertions(+), 11 deletions(-)

2011-05-05  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with parsing by multiple fetch modes
 src/blixemApp/blxFetch.c          |  18 +++++--
 src/blixemApp/blxmain.c           |   6 ++-
 src/blixemApp/blxview.c           | 103 +++++++++++++++++++++++++-------------
 src/seqtoolsUtils/blxGff3Parser.c |   2 +-
 4 files changed, 88 insertions(+), 41 deletions(-)

2011-05-04  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with fetch-by-mode. Also now specify that regions need data to be fetched.
 src/blixemApp/blxview.c           | 14 ++++++++------
 src/seqtoolsUtils/blxGff3Parser.c |  8 ++++++++
 src/seqtoolsUtils/blxmsp.c        | 17 +++++++++++++++--
 src/seqtoolsUtils/blxmsp.h        |  4 +++-
 4 files changed, 34 insertions(+), 9 deletions(-)

2011-05-04  Gemma Barson  <gb10@sanger.ac.uk>
 Moved source data from the MSP struct to the parent sequence struct
 src/blixemApp/blxview.c           | 13 +++++++-
 src/blixemApp/detailviewtree.c    | 14 ++++-----
 src/seqtoolsUtils/blxGff3Parser.c |  8 +----
 src/seqtoolsUtils/blxmsp.c        | 64 ++++++++++++++++++++++-----------------
 src/seqtoolsUtils/blxmsp.h        | 13 +++++---
 5 files changed, 64 insertions(+), 48 deletions(-)

2011-05-04  Gemma Barson  <gb10@sanger.ac.uk>
 Data type is now populated in the sequences
 src/blixemApp/blxview.c           |  4 ++++
 src/seqtoolsUtils/blxGff3Parser.c | 20 ++++++++++++++------
 src/seqtoolsUtils/blxmsp.c        | 18 +++++++++++++++---
 src/seqtoolsUtils/blxmsp.h        | 13 ++++---------
 src/seqtoolsUtils/blxparser.c     | 22 ++++++++++++++--------
 5 files changed, 51 insertions(+), 26 deletions(-)

2011-05-04  Gemma Barson  <gb10@sanger.ac.uk>
 Removed user-fetch mode from the data-type config group
 src/seqtoolsUtils/blxGff3Parser.c | 33 ---------------------------------
 src/seqtoolsUtils/blxmsp.c        | 27 +++++++++++++++++++++++++++
 src/seqtoolsUtils/blxmsp.h        |  3 ++-
 3 files changed, 29 insertions(+), 34 deletions(-)

2011-05-04  Gemma Barson  <gb10@sanger.ac.uk>
 Allow a differentiation between bulk-fetch mode and interactive/user-fetch mode in the config file
 src/blixemApp/blixem_.h           |  86 ++++++++++----------
 src/blixemApp/blxFetch.c          |  75 ++++++++++-------
 src/blixemApp/blxdotter.c         |   2 +-
 src/blixemApp/blxmain.c           |   7 +-
 src/blixemApp/blxview.c           | 166 +++++++++++++++++++++++++++++---------
 src/blixemApp/blxwindow.c         |  32 +++++---
 src/blixemApp/blxwindow.h         |   2 +-
 src/seqtoolsUtils/blxGff3Parser.c |  24 ++++--
 src/seqtoolsUtils/blxmsp.c        |   1 +
 src/seqtoolsUtils/blxmsp.h        |  23 ++++--
 10 files changed, 281 insertions(+), 137 deletions(-)

2011-05-04  Gemma Barson  <gb10@sanger.ac.uk>
 Removed bulk-fetch mode to simplify initial implementation
 src/seqtoolsUtils/blxGff3Parser.c | 9 +--------
 src/seqtoolsUtils/blxmsp.h        | 1 -
 2 files changed, 1 insertion(+), 9 deletions(-)

2011-05-04  Gemma Barson  <gb10@sanger.ac.uk>
 Added data-type struct and populate it in MSPs that have a data-type specified
 src/blixemApp/blxFetch.c          |   1 -
 src/blixemApp/blxmain.c           |   4 +-
 src/dotterApp/dotterMain.c        |   2 +-
 src/seqtoolsUtils/blxGff3Parser.c | 109 ++++++++++++++++++++++++++++++++++++--
 src/seqtoolsUtils/blxGff3Parser.h |   3 +-
 src/seqtoolsUtils/blxmsp.h        |  12 ++++-
 src/seqtoolsUtils/blxparser.c     |  13 ++---
 src/seqtoolsUtils/blxparser.h     |   2 +-
 8 files changed, 129 insertions(+), 17 deletions(-)

2011-05-03  Gemma Barson  <gb10@sanger.ac.uk>
 Removed commented out code
 src/blixemApp/blxFetch.c | 84 +++++++++++++++++++++---------------------------
 1 file changed, 37 insertions(+), 47 deletions(-)

2011-05-03  Gemma Barson  <gb10@sanger.ac.uk>
 Always initialise pfetch node and port on startup
 src/blixemApp/blxFetch.c | 18 +++---------------
 1 file changed, 3 insertions(+), 15 deletions(-)

2011-05-03  Gemma Barson  <gb10@sanger.ac.uk>
 Added new fetch method groups for config file
 src/blixemApp/blixem_.h    |  20 ++++++--
 src/blixemApp/blxFetch.c   | 125 ++++++++++++++++++++++++++++-----------------
 src/blixemApp/blxview.c    |   2 +-
 src/seqtoolsUtils/blxmsp.h |   6 ++-
 4 files changed, 99 insertions(+), 54 deletions(-)

2011-05-03  Gemma Barson  <gb10@sanger.ac.uk>
 Added 'region' to supported GFF types
 src/seqtoolsUtils/blxGff3Parser.c | 25 ++++++++++++++++++-------
 src/seqtoolsUtils/blxmsp.h        | 18 ++++++++++++------
 2 files changed, 30 insertions(+), 13 deletions(-)

2011-05-26  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.19
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-05-26  Gemma Barson  <gb10@sanger.ac.uk>
 Reading frame is now calculated from the mapped coords rather than the original coords
 src/blixemApp/blxview.c    | 122 +----------------------------------------
 src/dotterApp/dotterMain.c |   2 +-
 src/seqtoolsUtils/blxmsp.c | 131 +++++++++++++++++++++++++++++++++++++++++++--
 src/seqtoolsUtils/blxmsp.h |   2 +-
 4 files changed, 130 insertions(+), 127 deletions(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Updated user manual with new command-line arguments
 src/doc/User_doc/Blixem_manual.odt | Bin 1095685 -> 1095666 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 849220 -> 849234 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Updated usage text in user pages
 src/doc/User_doc/blixem_usage.txt | 76 ++++++++++++++++++++-------------------
 1 file changed, 40 insertions(+), 36 deletions(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.18
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the --invert-sort option
 src/blixemApp/blxwindow.c | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the hide-big-picture option
 src/blixemApp/blxmain.c   |  2 +-
 src/blixemApp/blxwindow.c | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 dotter-first-match now finds the correct sequence to dotter
 src/blixemApp/blxview.c    | 27 ++++++++++++++++++---------
 src/blixemApp/detailview.c | 25 +++++++++++++++----------
 src/blixemApp/detailview.h |  8 ++++----
 3 files changed, 37 insertions(+), 23 deletions(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixes to do with --dotter-first-match option
 src/blixemApp/blxdotter.c | 2 +-
 src/blixemApp/blxview.c   | 6 ++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the dotter-first-match argument
 src/blixemApp/blxmain.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed bugs with command-line arguments, and implemented --map-coords
 src/blixemApp/blxmain.c | 42 +++++++++++++++++++++++++++++++-----------
 1 file changed, 31 insertions(+), 11 deletions(-)

2011-05-09  Gemma Barson  <gb10@sanger.ac.uk>
 Changed command-line arguments and added new --map-coords argument
 src/blixemApp/blixem_.h |   3 +
 src/blixemApp/blxmain.c | 202 ++++++++++++++++++++----------------------------
 2 files changed, 85 insertions(+), 120 deletions(-)

2011-04-14  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.17
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-04-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where start coord was not being bounds checked
 src/blixemApp/detailview.c | 5 +++++
 1 file changed, 5 insertions(+)

2011-04-14  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.16
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-04-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression where the initial display range was being overwritten
 src/blixemApp/detailview.c | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

2011-04-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression where Blixem was not centering on the start coord
 src/blixemApp/detailview.c | 25 +++++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

2011-04-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression where Blixem was not using the start coord correctly
 src/blixemApp/detailview.c | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

2011-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.15
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where there are gaps in the dotter crosshair when the labels are long
 src/dotterApp/dotplot.c          | 12 ++++--------
 src/dotterApp/seqtoolsExonView.c |  4 ++--
 2 files changed, 6 insertions(+), 10 deletions(-)

2011-04-05  Gemma Barson  <gb10@sanger.ac.uk>
 Updated user manuals
 src/doc/User_doc/Blixem_manual.odt | Bin 1065015 -> 1095685 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 822416 -> 849220 bytes
 src/doc/User_doc/Dotter_manual.odt | Bin 375921 -> 434335 bytes
 src/doc/User_doc/Dotter_manual.pdf | Bin 328787 -> 378981 bytes
 4 files changed, 0 insertions(+), 0 deletions(-)

2011-04-04  Gemma Barson  <gb10@sanger.ac.uk>
 Updated what's-new help pages
 src/doc/User_doc/blixem_news.html | 10 ++++++++++
 src/doc/User_doc/dotter_news.html |  7 +++++++
 2 files changed, 17 insertions(+)

2011-04-04  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression with calculating the display coords for exons
 src/blixemApp/blxview.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

2011-04-01  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to scrolling the big picture when the highlight box reaches the edge of the range
 src/blixemApp/bigpicture.c | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)

2011-03-31  Gemma Barson  <gb10@sanger.ac.uk>
 Updated test plan
 src/doc/Design_notes/testing.ods | Bin 30658 -> 35579 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2011-03-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with sorting when no columns are specified to sort by
 src/blixemApp/blxwindow.c      |  3 ++-
 src/blixemApp/detailviewtree.c | 19 +++++++++++++++----
 2 files changed, 17 insertions(+), 5 deletions(-)

2011-03-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with find-again not working correctly after a group operation
 src/blixemApp/blxwindow.c | 63 ++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 48 insertions(+), 15 deletions(-)

2011-03-31  Gemma Barson  <gb10@sanger.ac.uk>
 Removed a 'feature' where typing would bring up a text box on the detail view
 src/blixemApp/detailviewtree.c | 1 +
 1 file changed, 1 insertion(+)

2011-03-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the highlight box was getting out of position when zooming
 src/blixemApp/bigpicture.c | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

2011-03-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with filtering rows
 src/blixemApp/detailview.c | 35 +++++++++++++++++------------------
 1 file changed, 17 insertions(+), 18 deletions(-)

2011-03-30  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to Blixem menu and toolbar
 src/blixemApp/blxwindow.c      | 223 +++++++++++++++++++++++++++++++--------
 src/blixemApp/detailview.c     | 230 +++++++----------------------------------
 src/blixemApp/detailview.h     |   1 +
 src/blixemApp/detailviewtree.c |  73 +++++++------
 src/seqtoolsUtils/utilities.c  |  66 ------------
 src/seqtoolsUtils/utilities.h  |   2 -
 6 files changed, 257 insertions(+), 338 deletions(-)

2011-03-30  Gemma Barson  <gb10@sanger.ac.uk>
 Added accelerators to dotter context menu
 src/dotterApp/dotter.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-03-30  Gemma Barson  <gb10@sanger.ac.uk>
 Added icon to delete-all-groups button
 src/blixemApp/blxwindow.c | 1 +
 1 file changed, 1 insertion(+)

2011-03-30  Gemma Barson  <gb10@sanger.ac.uk>
 Added the option to hide all sequences that are not in a group
 src/blixemApp/blixem_.h        |   1 +
 src/blixemApp/blxwindow.c      | 135 +++++++++++++++++++++++++++--------------
 src/blixemApp/detailviewtree.c |  18 +++++-
 3 files changed, 107 insertions(+), 47 deletions(-)

2011-04-04  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'shortread'
2011-03-30  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with bad error propagation for find-by-list
 src/blixemApp/blxwindow.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2011-03-30  Gemma Barson  <gb10@sanger.ac.uk>
 Filtered out non-searchable columns from the search-by-column combo box
 src/blixemApp/blxwindow.c  | 25 ++++++++++++++++---------
 src/blixemApp/detailview.c | 26 ++++++++++++++------------
 src/blixemApp/detailview.h |  1 +
 3 files changed, 31 insertions(+), 21 deletions(-)

2011-03-30  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: Implemented search for different columns, not just the Name column
 src/blixemApp/blxwindow.c  | 393 ++++++++++++++++++++++++++++++++-------------
 src/blixemApp/blxwindow.h  |   2 +-
 src/blixemApp/detailview.c |  15 ++
 src/blixemApp/detailview.h |   1 +
 src/seqtoolsUtils/blxmsp.c |  15 +-
 src/seqtoolsUtils/blxmsp.h |   9 +-
 6 files changed, 313 insertions(+), 122 deletions(-)

2011-03-30  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: added search-by-column option to the Find and Group dialogs
 src/blixemApp/blxwindow.c | 90 +++++++++++++++++++++++++++++++----------------
 1 file changed, 60 insertions(+), 30 deletions(-)

2011-03-29  Gemma Barson  <gb10@sanger.ac.uk>
 Moved 'invert sort order' option from the Settings dialog to the Sort dialog
 src/blixemApp/blxwindow.c | 37 ++++++++++++++++++++++++-------------
 1 file changed, 24 insertions(+), 13 deletions(-)

2011-03-29  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with sorting short-reads when 'squash matches' is enabled
 src/blixemApp/detailviewtree.c | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

2011-03-29  Gemma Barson  <gb10@sanger.ac.uk>
 Added the ability to sort by multiple columns
 src/blixemApp/blixem_.h        |   4 +-
 src/blixemApp/blxmain.c        |   2 +-
 src/blixemApp/blxwindow.c      | 263 +++++++++++++++++++++++++++++++++++++++++
 src/blixemApp/blxwindow.h      |   1 +
 src/blixemApp/detailview.c     | 142 +++++++---------------
 src/blixemApp/detailviewtree.c |  61 +++++++---
 6 files changed, 353 insertions(+), 120 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Made sort box have a tear-off drop-down menu
 src/blixemApp/detailview.c | 2 ++
 1 file changed, 2 insertions(+)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Small change to separate handle-box creation from toolbar creation
 src/seqtoolsUtils/utilities.c | 22 ++++++++++++++++------
 src/seqtoolsUtils/utilities.h |  1 +
 2 files changed, 17 insertions(+), 6 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the dotter crosshair was not being redrawn correctly after printing
 src/dotterApp/dotplot.c | 7 +++++++
 1 file changed, 7 insertions(+)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the alignment tool was not being cleared before redrawing
 src/dotterApp/alignmenttool.c | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to Dotter menus
 src/dotterApp/dotter.c | 28 +++++++++++++++-------------
 1 file changed, 15 insertions(+), 13 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Shortened Dotter's context menu
 src/dotterApp/dotter.c | 97 ++++++++++++++++++--------------------------------
 1 file changed, 34 insertions(+), 63 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Changed sorting functions to allow for sorting by multiple columns
 src/blixemApp/blxwindow.c      |   1 -
 src/blixemApp/detailview.c     |  26 ++++-
 src/blixemApp/detailview.h     |   2 +
 src/blixemApp/detailviewtree.c | 210 +++++++++++++++++++++++------------------
 src/blixemApp/detailviewtree.h |   1 -
 5 files changed, 144 insertions(+), 96 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Removed an unnecessary call to refilter the tree rows
 src/blixemApp/detailview.c | 4 ----
 1 file changed, 4 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Performance improvements to row selections
 src/blixemApp/blxwindow.c | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where short reads from different strands were being counted as duplicates
 src/seqtoolsUtils/blxmsp.c | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed another memory leak
 src/dotterApp/dotterMain.c | 27 ++++++++++++++++++---------
 1 file changed, 18 insertions(+), 9 deletions(-)

2011-03-28  Gemma Barson  <gb10@sanger.ac.uk>
 Don't draw duplicate, overlapping MSPs
 src/blixemApp/sequencecellrenderer.c | 8 ++++++++
 1 file changed, 8 insertions(+)

2011-03-25  Gemma Barson  <gb10@sanger.ac.uk>
 More memory leak fixes
 src/blixemApp/detailviewtree.c | 11 +++++++----
 src/dotterApp/dotplot.c        |  3 +++
 src/dotterApp/greyramptool.c   |  2 ++
 src/seqtoolsUtils/utilities.c  |  6 +++++-
 4 files changed, 17 insertions(+), 5 deletions(-)

2011-03-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed more memory leaks
 src/blixemApp/coverageview.c         | 7 +++++--
 src/blixemApp/sequencecellrenderer.c | 3 +++
 src/dotterApp/greyramptool.c         | 3 +++
 src/seqtoolsUtils/utilities.c        | 3 +++
 4 files changed, 14 insertions(+), 2 deletions(-)

2011-03-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some memory leaks
 src/blixemApp/bigpicture.c           | 10 +++++++---
 src/blixemApp/bigpicturegrid.c       |  5 +++--
 src/blixemApp/blxdotter.c            | 11 ++++++-----
 src/blixemApp/blxmain.c              | 13 ++++++++-----
 src/blixemApp/coverageview.c         |  5 +++--
 src/blixemApp/detailview.c           | 18 ++++++++++++------
 src/blixemApp/detailviewtree.c       |  9 ++++++---
 src/blixemApp/exonview.c             |  5 ++++-
 src/blixemApp/sequencecellrenderer.c | 13 +++++++++++--
 src/dotterApp/alignmenttool.c        | 10 ++++++++++
 src/dotterApp/dotplot.c              | 36 +++++++++++++++++++++++++++++++-----
 src/dotterApp/greyramptool.c         |  8 +++++++-
 src/dotterApp/seqtoolsExonView.c     | 11 ++++++++---
 src/seqtoolsUtils/blxmsp.c           |  9 +++------
 src/seqtoolsUtils/blxparser.c        |  3 +--
 src/seqtoolsUtils/utilities.c        |  4 ++++
 16 files changed, 124 insertions(+), 46 deletions(-)

2011-03-25  Gemma Barson  <gb10@sanger.ac.uk>
 Performance improvements to scrolling
 src/blixemApp/bigpicture.c    | 20 +++++++++-----------
 src/blixemApp/blxwindow.c     | 10 ++++------
 src/blixemApp/exonview.c      |  6 +-----
 src/seqtoolsUtils/utilities.c |  7 +++++++
 src/seqtoolsUtils/utilities.h |  1 +
 5 files changed, 22 insertions(+), 22 deletions(-)

2011-03-24  Gemma Barson  <gb10@sanger.ac.uk>
 The big picture range now scrolls independently of the detail-view range
 src/blixemApp/bigpicture.c | 127 +++++++++++++++++++++++++++++++--------------
 src/blixemApp/bigpicture.h |   2 +-
 src/blixemApp/detailview.c |   4 +-
 3 files changed, 90 insertions(+), 43 deletions(-)

2011-04-04  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'shortread'
2011-03-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression where the highlight box was not being shown when printing
 src/blixemApp/bigpicture.c     | 15 +++++++++++++++
 src/blixemApp/bigpicture.h     |  1 +
 src/blixemApp/bigpicturegrid.c | 18 ++++++++++++++++++
 src/blixemApp/bigpicturegrid.h |  2 ++
 src/blixemApp/blxwindow.c      |  7 ++++++-
 src/blixemApp/coverageview.c   | 18 ++++++++++++++++++
 src/blixemApp/coverageview.h   |  2 ++
 src/blixemApp/exonview.c       | 18 ++++++++++++++++++
 src/blixemApp/exonview.h       |  2 ++
 src/dotterApp/alignmenttool.c  |  2 +-
 src/dotterApp/dotter.c         |  4 ++--
 src/seqtoolsUtils/utilities.c  | 41 +++++++++++++++++++++++++++++++++--------
 src/seqtoolsUtils/utilities.h  |  2 +-
 13 files changed, 119 insertions(+), 13 deletions(-)

2011-03-24  Gemma Barson  <gb10@sanger.ac.uk>
 Changed the highlight box to be truely transparent
 src/blixemApp/bigpicture.c     | 25 +++++++++----------------
 src/blixemApp/bigpicture.h     |  5 +----
 src/blixemApp/bigpicturegrid.c | 29 +++++++++--------------------
 src/blixemApp/bigpicturegrid.h |  2 --
 src/blixemApp/blxwindow.c      |  4 ++--
 src/blixemApp/coverageview.c   | 38 +++++++++++---------------------------
 src/blixemApp/coverageview.h   |  2 --
 src/blixemApp/exonview.c       | 33 ++++++++++-----------------------
 src/blixemApp/exonview.h       |  2 --
 src/seqtoolsUtils/utilities.c  | 18 +++++++-----------
 src/seqtoolsUtils/utilities.h  |  2 +-
 11 files changed, 50 insertions(+), 110 deletions(-)

2011-03-24  Gemma Barson  <gb10@sanger.ac.uk>
 Added the ability to adjust the coverage plot scale
 src/blixemApp/blxwindow.c    | 30 ++++++++++++++++++-
 src/blixemApp/coverageview.c | 71 +++++++++++++++++++++++++++++---------------
 src/blixemApp/coverageview.h |  5 ++++
 3 files changed, 81 insertions(+), 25 deletions(-)

2011-03-24  Gemma Barson  <gb10@sanger.ac.uk>
 Coverage view labels are now nice round values
 src/blixemApp/blxwindow.c    |  6 ++--
 src/blixemApp/coverageview.c | 82 ++++++++++++++++++++++++++++++++------------
 2 files changed, 63 insertions(+), 25 deletions(-)

2011-03-24  Gemma Barson  <gb10@sanger.ac.uk>
 Added middle-click scrolling to the coverage view
 src/blixemApp/bigpicture.c   |  4 ++
 src/blixemApp/coverageview.c | 91 +++++++++++++++++++++++++++++++++++++++++---
 src/blixemApp/coverageview.h |  3 +-
 3 files changed, 92 insertions(+), 6 deletions(-)

2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Made default coverage view height bigger
 src/blixemApp/coverageview.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Made source, score and ID columns show more sensible values when 'squash matches' is enabled
 src/blixemApp/detailviewtree.c | 82 ++++++++++++++++++++++++++++++------------
 1 file changed, 60 insertions(+), 22 deletions(-)

2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Short reads now have a generic name, and they have a row count when 'squash matches' is enabled
 src/blixemApp/detailviewtree.c | 16 +++++++++++++-
 src/seqtoolsUtils/blxmsp.c     | 48 ++++++++++++++++++++++++++----------------
 src/seqtoolsUtils/blxmsp.h     |  1 -
 3 files changed, 45 insertions(+), 20 deletions(-)

2011-04-04  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'shortread'
2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Added ability to hide coverage view, and hide it by default
 src/blixemApp/bigpicture.c   | 6 ++++++
 src/blixemApp/bigpicture.h   | 1 +
 src/blixemApp/blxwindow.c    | 8 ++++++++
 src/blixemApp/coverageview.c | 1 -
 4 files changed, 15 insertions(+), 1 deletion(-)

2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to coverage view height calculation
 src/blixemApp/bigpicturegrid.c |  7 -------
 src/blixemApp/blxwindow.c      |  5 +++--
 src/blixemApp/coverageview.c   | 41 +++++++++++++++++++++++++----------------
 src/blixemApp/coverageview.h   |  4 +++-
 4 files changed, 31 insertions(+), 26 deletions(-)

2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Right-align grid labels
 src/blixemApp/bigpicture.c | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Added horizontal grid lines to coverage plot
 src/blixemApp/bigpicture.c     |  7 ++++---
 src/blixemApp/bigpicture.h     |  3 ++-
 src/blixemApp/bigpicturegrid.c |  2 +-
 src/blixemApp/coverageview.c   | 15 +++++++++++----
 4 files changed, 18 insertions(+), 9 deletions(-)

2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Made horizontal grid-line drawing function more generic
 src/blixemApp/bigpicture.c     | 97 ++++++++++++++++++++++++++++++++++++------
 src/blixemApp/bigpicture.h     |  7 +++
 src/blixemApp/bigpicturegrid.c | 75 +-------------------------------
 src/blixemApp/bigpicturegrid.h |  1 -
 4 files changed, 93 insertions(+), 87 deletions(-)

2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Added vertical grid lines and highlight box to coverage view
 src/blixemApp/bigpicture.c     |  98 ++++++++++++++++++++++++++++++-
 src/blixemApp/bigpicture.h     |   7 +++
 src/blixemApp/bigpicturegrid.c | 128 ++++++++++-------------------------------
 src/blixemApp/bigpicturegrid.h |   2 +-
 src/blixemApp/coverageview.c   |  52 ++++++++++++++---
 src/blixemApp/coverageview.h   |   3 +
 6 files changed, 181 insertions(+), 109 deletions(-)

2011-03-23  Gemma Barson  <gb10@sanger.ac.uk>
 Coverage plot is now a bar chart rather than a line graph
 src/blixemApp/coverageview.c  | 52 ++++++++++++++++++++++++++++++++-----------
 src/seqtoolsUtils/utilities.c | 20 ++++++++---------
 src/seqtoolsUtils/utilities.h |  2 +-
 3 files changed, 49 insertions(+), 25 deletions(-)

2011-03-22  Gemma Barson  <gb10@sanger.ac.uk>
 Added custom colour for coverage plot
 src/blixemApp/blixem_.h       | 1 +
 src/blixemApp/blxwindow.c     | 1 +
 src/blixemApp/coverageview.c  | 3 +++
 src/seqtoolsUtils/utilities.h | 1 +
 4 files changed, 6 insertions(+)

2011-03-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added depth-coverage view
 src/blixemApp/Makefile.am    |   2 +-
 src/blixemApp/bigpicture.c   |   6 +
 src/blixemApp/bigpicture.h   |   2 +
 src/blixemApp/blxwindow.c    |  10 ++
 src/blixemApp/coverageview.c | 324 +++++++++++++++++++++++++++++++++++++++++++
 src/blixemApp/coverageview.h |  52 +++++++
 6 files changed, 395 insertions(+), 1 deletion(-)

2011-04-04  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'shortread'
2011-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Idential short-read alignments are now treated as the same sequence
 src/seqtoolsUtils/blxGff3Parser.c |  12 ++--
 src/seqtoolsUtils/blxmsp.c        | 129 +++++++++++++++++++++++++++++---------
 src/seqtoolsUtils/blxmsp.h        |   3 +-
 src/seqtoolsUtils/utilities.c     |   6 ++
 src/seqtoolsUtils/utilities.h     |   1 +
 5 files changed, 113 insertions(+), 38 deletions(-)

2011-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a potential crash if sequence name is null
 src/blixemApp/detailviewtree.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

2011-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a potential crash with indexing the depth array
 src/blixemApp/blxwindow.c | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

2011-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with calculating the max depth
 src/blixemApp/blxwindow.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Added ability to calculate coverage depth
 src/blixemApp/blixem_.h   |  4 +++
 src/blixemApp/blxview.c   |  2 +-
 src/blixemApp/blxwindow.c | 71 +++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 76 insertions(+), 1 deletion(-)

2011-04-04  Gemma Barson  <gb10@sanger.ac.uk>
 Merge branch 'shortread'
2011-03-11  Gemma Barson  <gb10@sanger.ac.uk>
 Simplified row-filtering code
 src/blixemApp/detailview.c | 172 +++++++++++++++++++++++----------------------
 1 file changed, 89 insertions(+), 83 deletions(-)

2011-03-11  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with filtering rows after changing the sort order
 src/blixemApp/detailviewtree.c | 4 ++++
 1 file changed, 4 insertions(+)

2011-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with filtering rows when showing unaligned sequence or polyA tails
 src/blixemApp/blxview.c    |  7 +++++--
 src/blixemApp/blxwindow.c  | 22 ++++++++++++----------
 src/blixemApp/detailview.c | 25 +++++++++++++++++++------
 src/blixemApp/detailview.h |  2 +-
 src/dotterApp/dotterMain.c |  7 -------
 5 files changed, 37 insertions(+), 26 deletions(-)

2011-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with filtering after enabling squash matches
 src/blixemApp/detailviewtree.c | 1 +
 1 file changed, 1 insertion(+)

2011-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with filtering trees when zooming
 src/blixemApp/detailview.c | 4 ++++
 1 file changed, 4 insertions(+)

2011-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with filtering detail-view rows
 src/blixemApp/detailview.c | 34 +++++++++++++++++++++++++++++-----
 1 file changed, 29 insertions(+), 5 deletions(-)

2011-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where short reads were not shown in the big picture
 src/blixemApp/bigpicturegrid.c | 2 +-
 src/seqtoolsUtils/blxmsp.c     | 6 ++++++
 src/seqtoolsUtils/blxmsp.h     | 1 +
 3 files changed, 8 insertions(+), 1 deletion(-)

2011-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Added debug
 src/blixemApp/detailview.c | 2 ++
 1 file changed, 2 insertions(+)

2011-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Added debug
 src/blixemApp/detailview.c | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

2011-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed compile warnings
 src/blixemApp/bigpicturegrid.c       | 1 -
 src/blixemApp/blxdotter.c            | 1 -
 src/blixemApp/blxview.c              | 6 ++++++
 src/blixemApp/blxwindow.c            | 1 -
 src/blixemApp/detailview.c           | 2 +-
 src/blixemApp/detailviewtree.c       | 3 ++-
 src/blixemApp/exonview.c             | 2 --
 src/blixemApp/sequencecellrenderer.c | 1 +
 8 files changed, 10 insertions(+), 7 deletions(-)

2011-03-08  Gemma Barson  <gb10@sanger.ac.uk>
 Added comments
 src/seqtoolsUtils/blxmsp.c | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2011-03-08  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with calculating the max len of MSPs
 src/blixemApp/blxview.c    | 11 ++++++++---
 src/blixemApp/detailview.c |  4 +++-
 src/seqtoolsUtils/blxmsp.h |  5 ++++-
 3 files changed, 15 insertions(+), 5 deletions(-)

2011-03-08  Gemma Barson  <gb10@sanger.ac.uk>
 Removed an obsolete comment
 src/blixemApp/blxmain.c | 6 ------
 1 file changed, 6 deletions(-)

2011-03-08  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where show-unaligned-sequence was not updating the display
 src/blixemApp/blxwindow.c  | 7 ++++++-
 src/blixemApp/detailview.c | 5 +++--
 2 files changed, 9 insertions(+), 3 deletions(-)

2011-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: performance improvements to filtering tree rows
 src/blixemApp/blxview.c    |  6 +++-
 src/blixemApp/detailview.c | 83 ++++++++++++++++++++++++++++++++++++++--------
 src/seqtoolsUtils/blxmsp.c | 18 +++++++++-
 3 files changed, 91 insertions(+), 16 deletions(-)

2011-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: fixed a bug with filtering detail-view rows
 src/blixemApp/blxview.c    |  7 +++++++
 src/blixemApp/blxwindow.c  |  1 -
 src/dotterApp/dotterMain.c |  7 +++++++
 src/seqtoolsUtils/blxmsp.c | 23 +++++++++++++++++++++++
 src/seqtoolsUtils/blxmsp.h |  1 +
 5 files changed, 38 insertions(+), 1 deletion(-)

2011-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with drawing exon boundaries
 src/blixemApp/sequencecellrenderer.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: replaced MSP lists with arrays
 src/blixemApp/blixem_.h           |  4 +-
 src/blixemApp/blxmain.c           |  4 +-
 src/blixemApp/blxview.c           | 10 ++---
 src/blixemApp/blxwindow.c         |  9 ++--
 src/blixemApp/blxwindow.h         |  2 +-
 src/blixemApp/detailview.c        | 86 +++++++++++++++++++++------------------
 src/dotterApp/dotterMain.c        |  8 ++--
 src/seqtoolsUtils/blxGff3Parser.c |  4 +-
 src/seqtoolsUtils/blxGff3Parser.h |  2 +-
 src/seqtoolsUtils/blxmsp.c        | 56 +++++++++++++++----------
 src/seqtoolsUtils/blxmsp.h        | 11 +++--
 src/seqtoolsUtils/blxparser.c     | 34 ++++++++--------
 src/seqtoolsUtils/blxparser.h     |  2 +-
 13 files changed, 128 insertions(+), 104 deletions(-)

2011-03-07  Gemma Barson  <gb10@sanger.ac.uk>
 Performance improvements to filtering trees
 src/blixemApp/blixem_.h        |   3 +-
 src/blixemApp/blxview.c        |  15 +++-
 src/blixemApp/blxwindow.c      |  21 ++---
 src/blixemApp/detailview.c     | 155 +++++++++++++++++++++++++++++++-----
 src/blixemApp/detailview.h     |   1 +
 src/blixemApp/detailviewtree.c | 174 ++++++++++++++++++++++-------------------
 src/blixemApp/detailviewtree.h |   9 +--
 src/seqtoolsUtils/blxmsp.c     |  25 +++++-
 src/seqtoolsUtils/blxmsp.h     |  21 ++++-
 9 files changed, 302 insertions(+), 122 deletions(-)

2011-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 Small performance improvement
 src/blixemApp/bigpicturegrid.c | 5 +++++
 1 file changed, 5 insertions(+)

2011-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: removed some unused code
 src/seqtoolsUtils/blxmsp.c | 41 -----------------------------------------
 1 file changed, 41 deletions(-)

2011-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 WIP: code refactoring
 src/blixemApp/detailview.c | 20 ++++++++++--
 src/seqtoolsUtils/blxmsp.c | 80 +++++++++++++++++++++++++++++++++++++---------
 2 files changed, 82 insertions(+), 18 deletions(-)

2011-03-01  Gemma Barson  <gb10@sanger.ac.uk>
 Small performance improvements to big picture
 src/blixemApp/bigpicture.c     | 37 +++++++++++++++++++++-------
 src/blixemApp/bigpicture.h     |  1 +
 src/blixemApp/bigpicturegrid.c | 28 +++++++++++++++++----
 src/blixemApp/detailview.c     | 55 +++++++++++++++++++++++++++---------------
 src/blixemApp/exonview.c       | 27 ++++++++++++++++++---
 5 files changed, 111 insertions(+), 37 deletions(-)

2011-02-23  Gemma Barson  <gb10@sanger.ac.uk>
 Performance: use cached MSP display range wherever possible
 src/blixemApp/bigpicturegrid.c       |  14 +----
 src/blixemApp/blixem_.h              |   4 +-
 src/blixemApp/blxdotter.c            |   9 +--
 src/blixemApp/blxview.c              | 110 ++++++++++++++++++-----------------
 src/blixemApp/detailview.c           |   8 +--
 src/blixemApp/detailviewtree.c       |   2 +-
 src/blixemApp/exonview.c             |  19 ++----
 src/blixemApp/sequencecellrenderer.c |  15 ++---
 8 files changed, 79 insertions(+), 102 deletions(-)

2011-02-23  Gemma Barson  <gb10@sanger.ac.uk>
 Performance improvements: cache the display coords and the full extent coords of MSPs
 src/blixemApp/blixem_.h              | 29 +++++-------
 src/blixemApp/blxview.c              | 87 +++++++++++++++++++++++++++---------
 src/blixemApp/blxwindow.c            | 73 +++++++++++++++++++++++++-----
 src/blixemApp/blxwindow.h            |  2 +-
 src/blixemApp/detailview.c           | 19 +++++---
 src/blixemApp/detailview.h           |  2 +-
 src/blixemApp/detailviewtree.c       | 14 +-----
 src/blixemApp/sequencecellrenderer.c | 12 ++---
 src/seqtoolsUtils/blxmsp.c           |  8 +++-
 src/seqtoolsUtils/blxmsp.h           |  8 ++++
 10 files changed, 172 insertions(+), 82 deletions(-)

2011-02-22  Gemma Barson  <gb10@sanger.ac.uk>
 Performance improvements to tree row filtering
 src/blixemApp/blxwindow.c            | 14 ++++++--
 src/blixemApp/blxwindow.h            |  1 +
 src/blixemApp/detailviewtree.c       | 64 ++++++++++++++++--------------------
 src/blixemApp/sequencecellrenderer.c |  1 +
 4 files changed, 42 insertions(+), 38 deletions(-)

2011-02-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added basic functionality to show read pairs on the same strand
 src/blixemApp/detailviewtree.c |  2 +-
 src/seqtoolsUtils/blxmsp.c     | 21 +++++++++++++++++----
 2 files changed, 18 insertions(+), 5 deletions(-)

2011-02-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added short-read data type
 src/blixemApp/detailview.c           |  5 +++--
 src/blixemApp/detailviewtree.c       |  8 ++++----
 src/blixemApp/sequencecellrenderer.c |  2 +-
 src/seqtoolsUtils/blxGff3Parser.c    |  8 +++++---
 src/seqtoolsUtils/blxmsp.c           | 40 ++++++++++++++++++++++++++++--------
 src/seqtoolsUtils/blxmsp.h           |  6 +++++-
 6 files changed, 50 insertions(+), 19 deletions(-)

2011-04-04  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.14
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-03-25  Gemma Barson  <gb10@sanger.ac.uk>
 Added a link to the SeqTools website to the README file
 src/README | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-03-25  Gemma Barson  <gb10@sanger.ac.uk>
 Added a pointer from the NEWS file to the individual programs' news files.
 src/NEWS | 4 ++++
 1 file changed, 4 insertions(+)

2011-03-25  Gemma Barson  <gb10@sanger.ac.uk>
 Made usage text files plain text rather than html
 src/blixemApp/blxmain.c                            |  5 +++
 src/doc/User_doc/Makefile.am                       |  2 +-
 src/doc/User_doc/blixem_quick_start.html           |  2 +-
 .../{blixem_usage.html => blixem_usage.txt}        | 46 ++++++++------------
 src/doc/User_doc/dotter_quick_start.html           |  2 +-
 src/doc/User_doc/dotter_usage.html                 | 49 ----------------------
 src/doc/User_doc/dotter_usage.txt                  | 37 ++++++++++++++++
 src/doc/User_doc/index.html                        |  4 +-
 src/dotterApp/dotterMain.c                         |  4 ++
 9 files changed, 68 insertions(+), 83 deletions(-)

2011-03-25  Gemma Barson  <gb10@sanger.ac.uk>
 Updated release histories
 src/doc/User_doc/blixem_news.html | 37 +++++++++++++++++++++++++++++++++++--
 src/doc/User_doc/dotter_news.html | 30 +++++++++++++++++++++++++++++-
 2 files changed, 64 insertions(+), 3 deletions(-)

2011-03-25  Gemma Barson  <gb10@sanger.ac.uk>
 Updated user manuals
 src/doc/User_doc/Blixem_manual.odt       | Bin 1074086 -> 1065015 bytes
 src/doc/User_doc/Blixem_manual.pdf       | Bin 826653 -> 822416 bytes
 src/doc/User_doc/Dotter_manual.odt       | Bin 279132 -> 375921 bytes
 src/doc/User_doc/Dotter_manual.pdf       | Bin 216955 -> 328787 bytes
 src/doc/User_doc/dotter_quick_start.html |   2 ++
 5 files changed, 2 insertions(+)

2011-03-22  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an off-by-one bug in the alignment tool when the display starts at a negative coord
 src/dotterApp/dotter.c | 56 ++++++++++++++++++++++++++++++--------------------
 1 file changed, 34 insertions(+), 22 deletions(-)

2011-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a couple of typos in the documentation
 src/doc/User_doc/blixem_quick_start.html | 4 ++--
 src/doc/User_doc/dotter_quick_start.html | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

2011-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Added some missing help files to the installation
 src/doc/User_doc/Makefile.am | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

2011-03-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug in the runconfig script when prefix is not supplied
 src/runconfig.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

2011-03-16  Gemma Barson  <gb10@sanger.ac.uk>
 Added separate whats-new pages to the help
 src/doc/User_doc/blixem_news.html        | 25 +++++++++++++++++++++++++
 src/doc/User_doc/blixem_quick_start.html | 22 ++--------------------
 src/doc/User_doc/dotter_news.html        | 21 +++++++++++++++++++++
 src/doc/User_doc/dotter_quick_start.html | 17 ++---------------
 src/doc/User_doc/index.html              |  2 ++
 5 files changed, 52 insertions(+), 35 deletions(-)

2011-03-16  Gemma Barson  <gb10@sanger.ac.uk>
 Small change to documentation
 src/doc/Design_notes/specs.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-03-01  Gemma Barson  <gb10@sanger.ac.uk>
 Added documentation about printing
 src/doc/Design_notes/modules/seqtoolsUtils.html | 34 +++++++++++++++++++++----
 1 file changed, 29 insertions(+), 5 deletions(-)

2011-03-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the build system not linking libraries correctly
 src/Makefile.am               | 11 ++++++++---
 src/blixemApp/Makefile.am     |  2 +-
 src/dotterApp/Makefile.am     |  4 ++--
 src/seqtoolsUtils/Makefile.am |  1 -
 4 files changed, 11 insertions(+), 7 deletions(-)

2011-03-14  Gemma Barson  <gb10@sanger.ac.uk>
 The OpenOffice versions of the manuals had mistakenly been removed from the distribution
 src/doc/User_doc/Makefile.am | 3 +++
 1 file changed, 3 insertions(+)

2011-03-14  Gemma Barson  <gb10@sanger.ac.uk>
 Replaced the Help dialogs in Blixem and Dotter with html help files that open in a browser
 src/Makefile.am                          |   9 +-
 src/blixemApp/blixem_.h                  |   2 +-
 src/blixemApp/blxdotter.c                |  58 -----
 src/blixemApp/blxwindow.c                | 309 +++------------------------
 src/blixemApp/detailview.c               |   9 +-
 src/configure.ac                         |   2 +-
 src/doc/Makefile.am                      |   4 +
 src/doc/User_doc/Makefile.am             |   3 +
 src/doc/User_doc/blixem_quick_start.html | 350 +++++++++++++++++++++++++++++++
 src/doc/User_doc/blixem_usage.html       | 100 +++++++++
 src/doc/User_doc/dotter_quick_start.html |  91 ++++++++
 src/doc/User_doc/dotter_usage.html       |  49 +++++
 src/doc/User_doc/index.html              |  25 ++-
 src/doc/User_doc/manuals.html            |  18 ++
 src/doc/index.html                       |   2 +-
 src/dotterApp/dotter.c                   | 177 +++-------------
 src/dotterApp/dotter_.h                  |   2 +-
 src/seqtoolsUtils/utilities.c            |  63 ++++++
 src/seqtoolsUtils/utilities.h            |   1 +
 19 files changed, 777 insertions(+), 497 deletions(-)

2011-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.13
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed an issue where Dotter was overwriting the primary clipboard on startup
 src/dotterApp/greyramptool.c | 5 +++++
 1 file changed, 5 insertions(+)

2011-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Allow user to change the active reading frame by clicking a tree header
 src/blixemApp/detailviewtree.c | 3 +++
 1 file changed, 3 insertions(+)

2011-03-10  Gemma Barson  <gb10@sanger.ac.uk>
 Turned warnings on in default compiler options in runconfig
 src/runconfig.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-03-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed compiler warnings
 src/blixemApp/bigpicture.c     |  7 -------
 src/blixemApp/blxwindow.c      |  2 --
 src/blixemApp/detailview.c     |  8 --------
 src/blixemApp/detailviewtree.c | 30 +-----------------------------
 src/dotterApp/alignmenttool.c  |  1 -
 src/dotterApp/dotter.c         | 10 ++++++----
 src/dotterApp/greyramptool.c   |  2 --
 src/seqtoolsUtils/utilities.c  |  4 ----
 src/seqtoolsUtils/utilities.h  |  1 +
 9 files changed, 8 insertions(+), 57 deletions(-)

2011-03-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed path to GTK version in /software
 src/runconfig.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-03-01  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.12
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-03-01  Gemma Barson  <gb10@sanger.ac.uk>
 Added the ability to specify column widths in the config file
 src/blixemApp/detailview.c | 46 ++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 42 insertions(+), 4 deletions(-)

2011-03-01  Gemma Barson  <gb10@sanger.ac.uk>
 Made Source column sortable and reverted its width to 85 pixels
 src/blixemApp/detailview.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-03-01  Gemma Barson  <gb10@sanger.ac.uk>
 Added Source column to mouse-over feedback text
 src/seqtoolsUtils/blxmsp.c | 62 +++++++++++++++++++++++++++++++++-------------
 1 file changed, 45 insertions(+), 17 deletions(-)

2011-03-01  Gemma Barson  <gb10@sanger.ac.uk>
 Enable Source column by default and make it narrow
 src/blixemApp/detailview.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-02-18  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.11
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-02-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with populating optional data for protein variants
 src/blixemApp/blxview.c   | 31 +++++++++++++++++--------------
 src/blixemApp/blxwindow.c |  8 ++++++++
 2 files changed, 25 insertions(+), 14 deletions(-)

2011-02-18  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.10
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-02-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with splice sites being shown incorrectly at termini
 src/blixemApp/detailview.c     |  4 +--
 src/blixemApp/detailviewtree.c |  8 +++---
 src/seqtoolsUtils/blxmsp.c     | 65 ++++++++++++++++++++++++------------------
 src/seqtoolsUtils/blxmsp.h     |  9 +++---
 4 files changed, 49 insertions(+), 37 deletions(-)

2011-02-17  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash when dottering multiple sequences
 src/dotterApp/dotterMain.c | 76 +++++++++++++++++++++++++---------------------
 1 file changed, 42 insertions(+), 34 deletions(-)

2011-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Updated to-do list
 src/doc/Design_notes/todo.html | 1 +
 1 file changed, 1 insertion(+)

2011-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Updated test plan
 src/doc/Design_notes/testing.ods | Bin 31495 -> 30658 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2011-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where invalid UTR sections were sometimes being created
 src/seqtoolsUtils/blxmsp.c | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

2011-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with UTRs not always showing in the detail-view
 src/blixemApp/blxview.c    | 120 +++++++++++++++++++++++++++++++++++++++++++++
 src/blixemApp/blxwindow.c  | 116 -------------------------------------------
 src/seqtoolsUtils/blxmsp.c |  20 ++++----
 3 files changed, 130 insertions(+), 126 deletions(-)

2011-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Added shortcut tip for Close menu item on greyramp tool
 src/dotterApp/greyramptool.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-02-16  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a typo (incorrect keyboard shortcut tip)
 src/dotterApp/alignmenttool.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-02-15  Gemma Barson  <gb10@sanger.ac.uk>
 Removed some unnecessary calls to access object properties
 src/blixemApp/bigpicture.c | 49 ++++++++++++++++++++-------------------
 src/blixemApp/detailview.c | 57 ++++++++++++++++++++++++++++++----------------
 src/blixemApp/exonview.c   |  9 +++++---
 3 files changed, 69 insertions(+), 46 deletions(-)

2011-02-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with scrolling in Blixem
 src/blixemApp/blxwindow.c      | 16 ++++------
 src/blixemApp/detailview.c     | 67 ++++++++++++++++++++++++++++++++++++++++++
 src/blixemApp/detailview.h     |  3 ++
 src/blixemApp/detailviewtree.c | 48 ++++--------------------------
 4 files changed, 82 insertions(+), 52 deletions(-)

2011-02-14  Gemma Barson  <gb10@sanger.ac.uk>
 Added a note about the key file option to the Blixem user manual
 src/doc/User_doc/Blixem_manual.odt | Bin 1073400 -> 1074086 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 824490 -> 826653 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-02-14  Gemma Barson  <gb10@sanger.ac.uk>
 Updated to-do list
 src/doc/Design_notes/todo.html | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

2011-02-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a potential crash when bounds-checking dotter coords
 src/blixemApp/blxdotter.c | 36 +++++++++++++++++++++++++++---------
 1 file changed, 27 insertions(+), 9 deletions(-)

2011-02-11  Gemma Barson  <gb10@sanger.ac.uk>
 Updated to-do list
 src/doc/Design_notes/todo.html | 2 --
 1 file changed, 2 deletions(-)

2011-02-11  Gemma Barson  <gb10@sanger.ac.uk>
 Added options to dotter settings to turn breaklines on/off
 src/dotterApp/dotplot.c | 25 ++++++++++++++--
 src/dotterApp/dotter.c  | 79 +++++++++++++++++++++++++++++++++++++++++++++++++
 src/dotterApp/dotter_.h |  3 ++
 3 files changed, 105 insertions(+), 2 deletions(-)

2011-02-11  Gemma Barson  <gb10@sanger.ac.uk>
 Only provide space for breakline labels if applicable
 src/dotterApp/dotplot.c    | 64 +++++++++++++++++++++++++++++-----------------
 src/dotterApp/dotter.c     | 14 +++++++---
 src/dotterApp/dotter.h     |  2 +-
 src/dotterApp/dotterMain.c | 16 ++++++------
 src/dotterApp/dotter_.h    |  7 ++++-
 5 files changed, 65 insertions(+), 38 deletions(-)

2011-02-10  Gemma Barson  <gb10@sanger.ac.uk>
 Added breaklines for multiple sequences in Dotter
 src/dotterApp/dotplot.c    | 188 +++++++++++++++++++++++++++++++++++++++------
 src/dotterApp/dotter.c     |  10 ++-
 src/dotterApp/dotterMain.c |   2 +-
 src/dotterApp/dotter_.h    |   6 ++
 4 files changed, 177 insertions(+), 29 deletions(-)

2011-02-10  Gemma Barson  <gb10@sanger.ac.uk>
 Updated Dotter manual
 src/doc/User_doc/Dotter_manual.odt | Bin 278153 -> 279132 bytes
 src/doc/User_doc/Dotter_manual.pdf | Bin 259208 -> 216955 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-02-10  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to docs
 src/doc/Design_notes/build.html             |  1 +
 src/doc/Design_notes/modules/libpfetch.html |  3 +--
 src/doc/Design_notes/specs.html             | 21 +++++----------------
 src/doc/User_doc/index.html                 | 18 ++++++++++++++++++
 src/doc/index.html                          | 16 ++++++++++++++++
 5 files changed, 41 insertions(+), 18 deletions(-)

2011-02-09  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a potential crash where the name column is too narrow to display the abbreviated name
 src/blixemApp/detailviewtree.c | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

2011-02-08  Gemma Barson  <gb10@sanger.ac.uk>
 Don't allow printing to scale an image to be larger
 src/seqtoolsUtils/utilities.c | 1 +
 1 file changed, 1 insertion(+)

2011-02-08  Gemma Barson  <gb10@sanger.ac.uk>
 Alignment tool now refreshes when its size is changed
 src/dotterApp/alignmenttool.c | 9 +++++++++
 1 file changed, 9 insertions(+)

2011-02-08  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a typo (incorrect keyboard shortcut tip)
 src/dotterApp/alignmenttool.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-02-08  Gemma Barson  <gb10@sanger.ac.uk>
 Added the ability to print the alignment tool
 src/blixemApp/blxwindow.c        |  17 ---
 src/dotterApp/alignmenttool.c    | 142 ++++++++-----------
 src/dotterApp/dotplot.c          |  39 +++---
 src/dotterApp/dotter.c           | 291 +++++++++++++++++++++++----------------
 src/dotterApp/dotter_.h          |  11 +-
 src/dotterApp/greyramptool.c     |  27 ++--
 src/dotterApp/seqtoolsExonView.c |  10 +-
 src/seqtoolsUtils/utilities.c    |  27 ++++
 src/seqtoolsUtils/utilities.h    |   2 +
 9 files changed, 310 insertions(+), 256 deletions(-)

2011-02-08  Gemma Barson  <gb10@sanger.ac.uk>
 Printing from Dotter now includes the crosshair and labels
 src/dotterApp/dotplot.c          | 56 +++++++++++++++++++++++++++++++++-------
 src/dotterApp/dotter.c           | 35 +++++++++++++++++++++----
 src/dotterApp/dotter_.h          |  1 +
 src/dotterApp/seqtoolsExonView.c | 21 +++++++++++++++
 src/dotterApp/seqtoolsExonView.h |  1 +
 5 files changed, 99 insertions(+), 15 deletions(-)

2011-02-08  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with printing where background was not being cleared
 src/seqtoolsUtils/utilities.c | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

2011-02-07  Gemma Barson  <gb10@sanger.ac.uk>
 Removed page-setup option from Blixem menu
 src/blixemApp/blxwindow.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2011-02-07  Gemma Barson  <gb10@sanger.ac.uk>
 Added basic printing for Dotter
 src/blixemApp/blxwindow.c     | 36 ++----------------------------------
 src/dotterApp/dotter.c        | 32 +++++++++++++++++++++++++-------
 src/seqtoolsUtils/utilities.c | 39 +++++++++++++++++++++++++++++++++++++++
 src/seqtoolsUtils/utilities.h |  2 ++
 4 files changed, 68 insertions(+), 41 deletions(-)

2011-02-07  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with printing in Blixem where label background colour was wrong
 src/blixemApp/detailviewtree.c | 1 +
 src/seqtoolsUtils/utilities.c  | 2 --
 2 files changed, 1 insertion(+), 2 deletions(-)

2011-02-07  Gemma Barson  <gb10@sanger.ac.uk>
 Removed some commented-out code
 src/blixemApp/blxFetch.c | 69 ------------------------------------------------
 1 file changed, 69 deletions(-)

2011-02-07  Gemma Barson  <gb10@sanger.ac.uk>
 Printing in Blixem now scales to fit to page
 src/blixemApp/blxwindow.c     | 93 ++++++++++++++-----------------------------
 src/seqtoolsUtils/utilities.c | 82 +++++++++++++++++++++++++++++++++++++-
 src/seqtoolsUtils/utilities.h |  5 +++
 3 files changed, 115 insertions(+), 65 deletions(-)

2011-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to printing in Blixem
 src/blixemApp/blxwindow.c     | 46 ++++---------------------------------------
 src/blixemApp/detailview.c    |  5 ++++-
 src/seqtoolsUtils/utilities.c | 37 +++++++++++++++++++++++-----------
 src/seqtoolsUtils/utilities.h |  2 +-
 4 files changed, 34 insertions(+), 56 deletions(-)

2011-02-04  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.9
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-02-04  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with pfetched sequences getting the wrong length
 src/blixemApp/blxdotter.c | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2011-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.8
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with unaligned sequence coords when display is reversed
 src/blixemApp/blxview.c | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

2011-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.7
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Added help for new navigation functionality in dotter
 src/dotterApp/dotter.c | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

2011-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with selecting variations in protein mode
 src/blixemApp/detailview.c     | 75 ++++++++++++++++--------------------------
 src/blixemApp/detailview.h     |  1 -
 src/blixemApp/detailviewtree.c |  2 +-
 3 files changed, 29 insertions(+), 49 deletions(-)

2011-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with calculating match seq coordinates for unaligned portions of sequence
 src/blixemApp/blixem_.h              |  84 +++++++++++--
 src/blixemApp/blxview.c              | 222 +++++++++++++++++++++--------------
 src/blixemApp/blxwindow.h            |  67 -----------
 src/blixemApp/detailview.c           |   2 +-
 src/blixemApp/sequencecellrenderer.c |   5 +-
 5 files changed, 214 insertions(+), 166 deletions(-)

2011-02-03  Gemma Barson  <gb10@sanger.ac.uk>
 Added convenience script to run ./configure with machine-specific arguments
 src/runconfig.sh | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

2011-02-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with dottering the reverse strand vs itself
 src/blixemApp/blxdotter.c  | 45 ++++++++++++++++++++++++++++++---------------
 src/dotterApp/dotplot.c    |  5 ++---
 src/dotterApp/dotter.c     |  2 +-
 src/dotterApp/dotterMain.c | 11 ++++++++---
 4 files changed, 41 insertions(+), 22 deletions(-)

2011-02-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where the selected coord was changing when the strand is toggled
 src/blixemApp/detailview.c | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

2011-02-02  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with go-to-position on the reverse strand
 src/blixemApp/detailview.c | 17 ++---------------
 1 file changed, 2 insertions(+), 15 deletions(-)

2011-02-01  Gemma Barson  <gb10@sanger.ac.uk>
 Updated to-do list
 src/doc/Design_notes/todo.html | 2 ++
 1 file changed, 2 insertions(+)

2011-02-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with dotter coords
 src/blixemApp/blxdotter.c | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

2011-02-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with dotter dialog coords when display reversed
 src/blixemApp/blxdotter.c | 113 +++++++++++++++++++++++++++++++++++++---------
 1 file changed, 92 insertions(+), 21 deletions(-)

2011-02-01  Gemma Barson  <gb10@sanger.ac.uk>
 Updated to-do list
 src/doc/Design_notes/todo.html | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

2011-01-24  Gemma Barson  <gb10@sanger.ac.uk>
 Updated to-do list
 src/doc/Design_notes/todo.html | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

2011-01-24  Gemma Barson  <gb10@sanger.ac.uk>
 Vertical exon view in Dotter is now working
 src/blixemApp/bigpicture.c       |   4 +-
 src/blixemApp/bigpicturegrid.c   |  10 ++--
 src/blixemApp/blixem_.h          |   1 -
 src/blixemApp/blxview.c          |  40 ----------------
 src/blixemApp/exonview.c         |   8 ++--
 src/dotterApp/seqtoolsExonView.c | 101 +++++++++++++++++++++++----------------
 src/seqtoolsUtils/blxmsp.c       |  53 ++++++++++++++++----
 src/seqtoolsUtils/blxmsp.h       |  10 ++--
 src/seqtoolsUtils/utilities.c    |  24 ++++++----
 src/seqtoolsUtils/utilities.h    |   1 +
 10 files changed, 136 insertions(+), 116 deletions(-)

2011-01-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression where introns were not being shown in Dotter
 src/seqtoolsUtils/blxmsp.c | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

2011-01-24  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with the vertical exon view in Dotter
 src/dotterApp/dotplot.c          | 12 ++++++++----
 src/dotterApp/dotter.c           |  8 ++++----
 src/dotterApp/seqtoolsExonView.c | 12 +++++++-----
 src/dotterApp/seqtoolsExonView.h |  3 ++-
 4 files changed, 21 insertions(+), 14 deletions(-)

2011-01-21  Gemma Barson  <gb10@sanger.ac.uk>
 Updated to-do list
 src/doc/Design_notes/todo.html | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

2011-01-21  Gemma Barson  <gb10@sanger.ac.uk>
 More work on the right-hand-side exon view in Dotter
 src/dotterApp/dotplot.c          |  4 ++--
 src/dotterApp/dotter.c           | 14 +++++++++----
 src/dotterApp/dotter_.h          |  3 +++
 src/dotterApp/seqtoolsExonView.c | 44 +++++++++++++++++++++++++++-------------
 4 files changed, 45 insertions(+), 20 deletions(-)

2011-01-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added exon view for vertical sequence in Dotter (WIP)
 src/blixemApp/blixem_.h          |   2 -
 src/blixemApp/blxdotter.c        | 168 ++++++++--------
 src/blixemApp/blxview.c          | 391 ------------------------------------
 src/dotterApp/dotplot.c          | 173 +++++++++++-----
 src/dotterApp/dotterMain.c       |  13 +-
 src/dotterApp/dotter_.h          |  38 ++--
 src/dotterApp/seqtoolsExonView.c |  23 ++-
 src/dotterApp/seqtoolsExonView.h |   2 +-
 src/seqtoolsUtils/blxmsp.c       | 418 +++++++++++++++++++++++++++++++++++++--
 src/seqtoolsUtils/blxmsp.h       |   6 +-
 10 files changed, 672 insertions(+), 562 deletions(-)

2011-02-01  Gemma Barson  <gb10@sanger.ac.uk>
 Added ability to copy coords from dotter
 src/dotterApp/alignmenttool.c | 31 +++++++++++++++++++++++++++++--
 src/dotterApp/dotter.c        | 40 +++++++++++++++++++++++++++++++++++++++-
 src/dotterApp/dotter_.h       |  1 +
 3 files changed, 69 insertions(+), 3 deletions(-)

2011-02-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression with the alignment tool
 src/dotterApp/alignmenttool.c | 4 ++--
 src/dotterApp/dotter_.h       | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

2011-02-01  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the alignment tool coords for the reverse strand in protein mode
 src/dotterApp/alignmenttool.c | 81 ++++++++++++++++++++-----------------------
 src/dotterApp/dotter.c        | 62 ++++++++++++++-------------------
 src/dotterApp/dotter_.h       |  1 -
 3 files changed, 64 insertions(+), 80 deletions(-)

2011-01-31  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with sub-dottering a self-comparison
 src/dotterApp/dotplot.c | 12 +++++++-----
 src/dotterApp/dotter.c  | 21 ++++++++++-----------
 src/dotterApp/dotter_.h |  2 +-
 3 files changed, 18 insertions(+), 17 deletions(-)

2011-01-27  Gemma Barson  <gb10@sanger.ac.uk>
 Display CDS/UTR features from the same exon on the same row
 src/blixemApp/detailview.c     | 2 +-
 src/blixemApp/detailviewtree.c | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

2011-01-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug where out-of-range exons were being displayed
 src/blixemApp/sequencecellrenderer.c | 48 +++++++++++++++++++++---------------
 1 file changed, 28 insertions(+), 20 deletions(-)

2011-01-27  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a regression with moving the selected coord in Blixem by one nucleotide
 src/blixemApp/blxwindow.c  | 48 ++++++++++------------------------------------
 src/blixemApp/detailview.c | 10 +++++-----
 src/blixemApp/detailview.h | 15 ++++++++++++++-
 3 files changed, 29 insertions(+), 44 deletions(-)

2011-01-27  Gemma Barson  <gb10@sanger.ac.uk>
 Tidied alignment tool coord code and fixed a bug where dotter was not exiting
 src/dotterApp/alignmenttool.c | 60 +++++--------------------------------------
 src/dotterApp/dotter.c        | 41 ++++++++++++++++++++++++-----
 2 files changed, 41 insertions(+), 60 deletions(-)

2011-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 Made alignment tool display same reading frame order as blixem
 src/dotterApp/alignmenttool.c | 77 +++++++++++++++++++++++++++----------------
 1 file changed, 49 insertions(+), 28 deletions(-)

2011-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 More improvements to alignment tool coord display
 src/dotterApp/alignmenttool.c | 28 ++-------------
 src/dotterApp/dotter.c        | 81 +++++++++++++++++++++++++++----------------
 2 files changed, 54 insertions(+), 55 deletions(-)

2011-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to alignment tool coord display
 src/dotterApp/alignmenttool.c | 43 +++++++------------------------------
 src/dotterApp/dotter.c        | 49 +++++++++++++++++++++++++++++++++++++++++++
 src/dotterApp/dotter_.h       |  3 +++
 3 files changed, 59 insertions(+), 36 deletions(-)

2011-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with scrolling in the alignment tool
 src/dotterApp/alignmenttool.c | 35 +++++++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 10 deletions(-)

2011-01-26  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.6
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-01-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash caused by the alignment tool indexing out of range
 src/dotterApp/alignmenttool.c | 97 +++++++++++++++++++++++--------------------
 1 file changed, 51 insertions(+), 46 deletions(-)

2011-01-25  Gemma Barson  <gb10@sanger.ac.uk>
 Renamed close/quit menu options and added Close option for greyramp tool
 src/dotterApp/alignmenttool.c |  2 +-
 src/dotterApp/dotter.c        | 18 +++++-----
 src/dotterApp/greyramptool.c  | 77 +++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 87 insertions(+), 10 deletions(-)

2011-01-25  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash when sub-dottering in dotter-vs-self
 src/dotterApp/dotplot.c | 1 +
 1 file changed, 1 insertion(+)

2011-01-25  Gemma Barson  <gb10@sanger.ac.uk>
 Added Close item to the Dotter right-click menu
 src/dotterApp/dotter.c | 1 +
 1 file changed, 1 insertion(+)

2011-01-21  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a performance issue with middle-dragging on the big picture
 src/blixemApp/bigpicture.c     | 31 +++++++++++++++++++------------
 src/blixemApp/bigpicture.h     |  4 +++-
 src/blixemApp/bigpicturegrid.c | 14 ++++++++++++--
 src/blixemApp/bigpicturegrid.h |  2 ++
 src/blixemApp/exonview.c       | 28 +++++++++++++++++++---------
 src/blixemApp/exonview.h       |  2 ++
 src/seqtoolsUtils/utilities.c  |  8 +++-----
 src/seqtoolsUtils/utilities.h  |  2 +-
 8 files changed, 61 insertions(+), 30 deletions(-)

2011-01-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with changing the range of a self-comparison in Dotter
 src/dotterApp/dotter.c | 32 ++++++++++++++++++++++++++------
 1 file changed, 26 insertions(+), 6 deletions(-)

2011-01-20  Gemma Barson  <gb10@sanger.ac.uk>
 Added 'negate coords' option to Dotter
 src/blixemApp/blxdotter.c     |   7 ++-
 src/blixemApp/blxmain.c       |   5 +-
 src/dotterApp/alignmenttool.c |  15 ++---
 src/dotterApp/dotplot.c       |  15 +++--
 src/dotterApp/dotter.c        | 140 +++++++++++++++++++++++++++++++++++++++---
 src/dotterApp/dotter.h        |   1 +
 src/dotterApp/dotterMain.c    |   5 +-
 src/dotterApp/dotter_.h       |   3 +
 8 files changed, 164 insertions(+), 27 deletions(-)

2011-01-20  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with the Dotter crosshair getting out of range
 src/dotterApp/dotter.c | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

2011-01-19  Gemma Barson  <gb10@sanger.ac.uk>
 Added to-do page to design notes
 src/doc/Design_notes/index.html |  1 +
 src/doc/Design_notes/todo.html  | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 36 insertions(+)

2011-01-19  Gemma Barson  <gb10@sanger.ac.uk>
 Updated test plan
 src/doc/Design_notes/testing.ods | Bin 26481 -> 31495 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

2011-01-19  Gemma Barson  <gb10@sanger.ac.uk>
 Make sure we save all Dotter parameters
 src/blixemApp/blxdotter.c | 31 +++++++++++++++++++++++++++++--
 src/blixemApp/blxwindow.c |  2 ++
 src/blixemApp/blxwindow.h |  4 +++-
 3 files changed, 34 insertions(+), 3 deletions(-)

2011-01-19  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a crash running Dotter in HSP-only mode
 src/dotterApp/dotplot.c | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

2011-01-19  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a const-cast warning
 src/dotterApp/dotter.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-01-19  Gemma Barson  <gb10@sanger.ac.uk>
 Limit the column size a user can enter in Blixem
 src/blixemApp/blxwindow.c | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

2011-01-19  Gemma Barson  <gb10@sanger.ac.uk>
 Added 'Close all Dotters' option to Blixem
 src/blixemApp/blxdotter.c  |  7 ++++---
 src/blixemApp/blxmain.c    |  2 +-
 src/blixemApp/blxwindow.c  | 34 ++++++++++++++++++++++++++++++++--
 src/dotterApp/dotterMain.c |  5 +++--
 4 files changed, 40 insertions(+), 8 deletions(-)

2011-01-19  Gemma Barson  <gb10@sanger.ac.uk>
 Added to design notes: calling dotter from blixem
 src/doc/Design_notes/modules/blixemApp.html | 35 ++++++++++++++++++++++++++---
 1 file changed, 32 insertions(+), 3 deletions(-)

2011-01-19  Gemma Barson  <gb10@sanger.ac.uk>
 Added Dotter manual to dist
 src/Makefile.am | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

2011-01-18  Gemma Barson  <gb10@sanger.ac.uk>
 Added user manual for Dotter
 src/doc/User_doc/Dotter_manual.odt | Bin 0 -> 278153 bytes
 src/doc/User_doc/Dotter_manual.pdf | Bin 0 -> 259208 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-01-18  Gemma Barson  <gb10@sanger.ac.uk>
 Added Close menu option in Dotter.
 src/dotterApp/dotter.c       | 60 +++++++++++++++++++++++++++++++++++++-------
 src/dotterApp/greyramptool.c |  2 +-
 2 files changed, 52 insertions(+), 10 deletions(-)

2011-01-18  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a typo in the Blixem manual
 src/doc/User_doc/Blixem_manual.odt | Bin 1073383 -> 1073400 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 824506 -> 824490 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-01-17  Gemma Barson  <gb10@sanger.ac.uk>
 Added design/user docs to dist
 src/Makefile.am | 2 ++
 1 file changed, 2 insertions(+)

2011-01-17  Gemma Barson  <gb10@sanger.ac.uk>
 Added user manual for Blixem
 src/doc/User_doc/Blixem_manual.odt | Bin 0 -> 1073383 bytes
 src/doc/User_doc/Blixem_manual.pdf | Bin 0 -> 824506 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

2011-01-17  Gemma Barson  <gb10@sanger.ac.uk>
 Added design docs
 src/doc/Design_notes/architecture.html          |  22 ++++
 src/doc/Design_notes/build.html                 |  50 +++++++++
 src/doc/Design_notes/index.html                 |  15 +++
 src/doc/Design_notes/modules/blixemApp.html     | 139 ++++++++++++++++++++++++
 src/doc/Design_notes/modules/dotterApp.html     |  83 ++++++++++++++
 src/doc/Design_notes/modules/libpfetch.html     |  13 +++
 src/doc/Design_notes/modules/seqtoolsUtils.html |  44 ++++++++
 src/doc/Design_notes/specs.html                 |  26 +++++
 src/doc/Design_notes/testing.ods                | Bin 0 -> 26481 bytes
 9 files changed, 392 insertions(+)

2011-01-14  Gemma Barson  <gb10@sanger.ac.uk>
 Added config directory for Autotools intermediate files
 src/configure.ac | 1 +
 1 file changed, 1 insertion(+)

2011-01-14  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.5
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-01-14  Gemma Barson  <gb10@sanger.ac.uk>
 Removed an unused variable
 src/blixemApp/detailview.c | 2 --
 1 file changed, 2 deletions(-)

2011-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fix size of feedback box so feedback area is larger
 src/blixemApp/detailview.c | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

2011-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with middle-click highlighting.
 src/blixemApp/detailview.c | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

2011-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Refresh columns properly after loading optional data.
 src/blixemApp/blxwindow.c | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

2011-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with calculating the Organism alias.
 src/blixemApp/blxview.c | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

2011-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Added help info for new column functionality.
 src/blixemApp/blxwindow.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Improvements to Blixem columns.
 src/blixemApp/blxwindow.c      | 26 +++++++++++++++++++++--
 src/blixemApp/detailview.c     | 48 +++++++++++++++++++++++++++---------------
 src/blixemApp/detailview.h     |  4 +++-
 src/blixemApp/detailviewtree.c | 19 ++++++++++++-----
 4 files changed, 72 insertions(+), 25 deletions(-)

2011-01-13  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug in the mouse-move handler for the greyramp tool.
 src/dotterApp/greyramptool.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-01-11  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.4
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2011-01-11  Gemma Barson  <gb10@sanger.ac.uk>
 Changes to colour scheme.
 src/blixemApp/blxwindow.c     | 32 ++++++++++++-------------
 src/dotterApp/dotter.c        |  6 ++---
 src/seqtoolsUtils/utilities.c |  4 ++--
 src/seqtoolsUtils/utilities.h | 55 +++++++++++++++++--------------------------
 4 files changed, 43 insertions(+), 54 deletions(-)

2011-01-10  Gemma Barson  <gb10@sanger.ac.uk>
 Allow negated coords in go-to-position dialog.
 src/blixemApp/detailview.c | 58 ++++++++++++++++++++++++++++++++++------------
 1 file changed, 43 insertions(+), 15 deletions(-)

2011-01-10  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed a bug with initialising the selected base index.
 src/blixemApp/blxwindow.c      |  6 +++---
 src/blixemApp/detailview.c     | 48 +++++++++++++++++++++++++++++++++++++-----
 src/blixemApp/detailview.h     |  5 +++++
 src/blixemApp/detailviewtree.c |  5 +++--
 4 files changed, 54 insertions(+), 10 deletions(-)

2011-01-07  Gemma Barson  <gb10@sanger.ac.uk>
 Small modification to the usage info
 src/blixemApp/blxmain.c | 3 +++
 1 file changed, 3 insertions(+)

2011-01-05  Gemma Barson  <gb10@sanger.ac.uk>
 Prefixed window titles with application name.
 src/blixemApp/blixem_.h       |   1 +
 src/blixemApp/blxFetch.c      |   9 +++-
 src/blixemApp/blxdotter.c     |   4 +-
 src/blixemApp/blxmain.c       |   6 ++-
 src/blixemApp/blxwindow.c     |  31 +++++------
 src/blixemApp/detailview.c    |   2 +-
 src/dotterApp/alignmenttool.c |   4 +-
 src/dotterApp/dotter.c        | 123 ++++++++++++++++--------------------------
 src/dotterApp/dotter.h        |  46 ++--------------
 src/dotterApp/dotterMain.c    |  24 ++++-----
 src/dotterApp/dotter_.h       |   2 +
 src/dotterApp/greyramptool.c  |   2 +-
 src/seqtoolsUtils/utilities.c |  23 +++++---
 src/seqtoolsUtils/utilities.h |   1 +
 14 files changed, 113 insertions(+), 165 deletions(-)

2011-01-04  Gemma Barson  <gb10@sanger.ac.uk>
 Added to-do comment
 src/seqtoolsUtils/blxmsp.c | 5 +++++
 1 file changed, 5 insertions(+)

2010-12-23  Gemma Barson  <gb10@sanger.ac.uk>
 Updated source file header comments
 src/blixemApp/bigpicture.c             |  39 ++++++++--
 src/blixemApp/bigpicture.h             |  45 ++++++++++--
 src/blixemApp/bigpicturegrid.c         |  40 +++++++++--
 src/blixemApp/bigpicturegrid.h         |  45 ++++++++++--
 src/blixemApp/blixem_.h                |  38 +++++-----
 src/blixemApp/blxFetch.c               |  42 +++++------
 src/blixemApp/blxdotter.c              |  39 ++++++++--
 src/blixemApp/blxdotter.h              |  54 +++++++++++---
 src/blixemApp/blxmain.c                |  39 +++++-----
 src/blixemApp/blxview.c                | 125 +++++++++------------------------
 src/blixemApp/blxview.h                |  39 +++++-----
 src/blixemApp/blxwindow.c              |  39 ++++++++--
 src/blixemApp/blxwindow.h              |  44 ++++++++++--
 src/blixemApp/detailview.c             |  39 ++++++++--
 src/blixemApp/detailview.h             |  48 +++++++++++--
 src/blixemApp/detailviewtree.c         |  40 +++++++++--
 src/blixemApp/detailviewtree.h         |  54 ++++++++++++--
 src/blixemApp/exonview.c               |  39 ++++++++--
 src/blixemApp/exonview.h               |  41 +++++++++--
 src/blixemApp/sequencecellrenderer.c   |  40 +++++++++--
 src/blixemApp/sequencecellrenderer.h   |  50 +++++++++++--
 src/dotterApp/alignmenttool.c          |  46 ++++++++++--
 src/dotterApp/dotplot.c                |  41 +++++++++--
 src/dotterApp/dotter.c                 | 119 +++++++------------------------
 src/dotterApp/dotter.h                 |  36 ++++++----
 src/dotterApp/dotterKarlin.c           |  43 +++++++-----
 src/dotterApp/dotterMain.c             |  39 +++++-----
 src/dotterApp/dotter_.h                |  37 +++++-----
 src/dotterApp/greyramptool.c           |  43 ++++++++++--
 src/dotterApp/seqtoolsExonView.c       |  39 ++++++++--
 src/dotterApp/seqtoolsExonView.h       |  47 +++++++++++--
 src/seqtoolsUtils/blxGff3Parser.c      |  32 ++++++---
 src/seqtoolsUtils/blxGff3Parser.h      |  32 ++++++---
 src/seqtoolsUtils/blxmsp.c             |  40 +++++++++--
 src/seqtoolsUtils/blxmsp.h             |  48 +++++++++++--
 src/seqtoolsUtils/blxparser.c          |  45 ++++++------
 src/seqtoolsUtils/blxparser.h          |  48 ++++++++++---
 src/seqtoolsUtils/iupac.h              |  35 +++++----
 src/seqtoolsUtils/seqtoolsWebBrowser.c |  36 ++++++----
 src/seqtoolsUtils/translate.c          |  42 ++++++-----
 src/seqtoolsUtils/utilities.c          |  39 ++++++++--
 src/seqtoolsUtils/utilities.h          |  39 ++++++++--
 src/seqtoolsUtils/version.h            |  32 +++++----
 43 files changed, 1365 insertions(+), 572 deletions(-)

2010-12-21  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.3
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-12-21  Gemma Barson  <gb10@sanger.ac.uk>
 Made --compiled flag output to stdout so build script can pick it up
 src/blixemApp/blxmain.c    | 4 ++--
 src/dotterApp/dotterMain.c | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

2010-12-21  Gemma Barson  <gb10@sanger.ac.uk>
 Added --compiled option to blixem and dotter
 src/blixemApp/blxmain.c    | 18 ++++++++++++++++++
 src/dotterApp/dotterMain.c | 26 +++++++++++++++++++++-----
 2 files changed, 39 insertions(+), 5 deletions(-)

2010-12-16  Gemma Barson  <gb10@sanger.ac.uk>
 Added long options to dotter
 src/blixemApp/blxmain.c    |  4 +--
 src/dotterApp/dotterMain.c | 64 +++++++++++++++++++++++++++++++++++++++++-----
 2 files changed, 59 insertions(+), 9 deletions(-)

2010-12-16  Gemma Barson  <gb10@sanger.ac.uk>
 Improved Blixem and Dotter usage text
 src/blixemApp/blixem_.h    |   1 -
 src/blixemApp/blxmain.c    |  16 +++---
 src/blixemApp/blxview.c    |   5 --
 src/blixemApp/blxwindow.c  |   2 +-
 src/dotterApp/dotter.c     |   1 -
 src/dotterApp/dotterMain.c | 129 ++++++++++++++++++++++++---------------------
 6 files changed, 79 insertions(+), 75 deletions(-)

2010-12-16  Gemma Barson  <gb10@sanger.ac.uk>
 Improved Blixem usage text
 src/blixemApp/blixem_.h     |  5 ++-
 src/blixemApp/blxmain.c     | 89 ++++++++++++++++++++++++++++++++++-----------
 src/dotterApp/dotter_.h     |  5 ++-
 src/seqtoolsUtils/version.h | 10 +++++
 4 files changed, 83 insertions(+), 26 deletions(-)

2010-12-15  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version to 4.1.2
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-12-15  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with dotter batch mode
 src/dotterApp/dotplot.c | 189 ++++++++++++++++++++++--------------------------
 src/dotterApp/dotter.c  |  40 +++++++---
 src/dotterApp/dotter_.h |  45 +++++++++++-
 3 files changed, 159 insertions(+), 115 deletions(-)

2010-12-14  Gemma Barson  <gb10@sanger.ac.uk>
 Fixed some bugs with loading dotter plots. Created a new dotplot file format '3' because the zoom factor has changed from an int to a double.
 src/dotterApp/dotplot.c      | 203 +++++++++++++++++++++++++++----------------
 src/dotterApp/dotterKarlin.c |   9 +-
 src/dotterApp/dotter_.h      |   2 +-
 3 files changed, 133 insertions(+), 81 deletions(-)

2010-12-07  Gemma Barson  <gb10@sanger.ac.uk>
 Increased version number to 4.1.1
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-12-07  Gemma Barson  <gb10@sanger.ac.uk>
 Blixem and Dotter now use the package version number, which is specified in version.m4.  I upped this to 4.1.0 so that it is a sensible progression for each program (blixem from 4.0.4 and dotter from 4.0.0).
 src/blixemApp/blixem_.h     |  28 +++++-------
 src/blixemApp/blxmain.c     |   2 +-
 src/blixemApp/blxwindow.c   |   4 +-
 src/dotterApp/dotter.c      |   4 +-
 src/dotterApp/dotterMain.c  |   2 +-
 src/dotterApp/dotter_.h     |  27 +++++------
 src/seqtoolsUtils/version.h | 106 ++++++++++++++++++++++++++------------------
 src/version.m4              |   2 +-
 8 files changed, 91 insertions(+), 84 deletions(-)

2010-12-06  Gemma Barson  <gb10@sanger.ac.uk>
 Incremented version number
 src/version.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-12-06  Gemma Barson  <gb10@sanger.ac.uk>
 Added version.m4 file to control package version number
 src/configure.ac | 4 +++-
 src/version.m4   | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

2010-11-30  Gemma Barson  <gb10@sanger.ac.uk>
 Set initial version number for the SeqTools package
 src/configure.ac | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-11-29  Gemma Barson  <gb10@sanger.ac.uk>
 Small change to the README file
 src/README | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2010-11-29  Gemma Barson  <gb10@sanger.ac.uk>
 Small change to the AUTHORS file
 src/AUTHORS | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-11-29  Gemma Barson  <gb10@sanger.ac.uk>
 Added gitignore file
 .gitignore | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

2010-11-26  Gemma Barson  <gb10@sanger.ac.uk>
 Changed includes etc. to work with the new build system
 src/blixemApp/bigpicture.c             |  10 +--
 src/blixemApp/bigpicture.h             |   6 +-
 src/blixemApp/bigpicturegrid.c         |  12 +--
 src/blixemApp/bigpicturegrid.h         |   4 +-
 src/blixemApp/blixem_.h                |  55 +------------
 src/blixemApp/blxFetch.c               |  10 +--
 src/blixemApp/blxdotter.c              |  39 +++++----
 src/blixemApp/blxmain.c                |  12 +--
 src/blixemApp/blxview.c                |  18 ++---
 src/blixemApp/blxwindow.c              |  20 ++---
 src/blixemApp/blxwindow.h              |   4 +-
 src/blixemApp/detailview.c             |  18 ++---
 src/blixemApp/detailview.h             |   4 +-
 src/blixemApp/detailviewtree.c         |  14 ++--
 src/blixemApp/detailviewtree.h         |   6 +-
 src/blixemApp/exonview.c               |  16 ++--
 src/blixemApp/exonview.h               |   2 +-
 src/blixemApp/sequencecellrenderer.c   |  30 +++----
 src/blixemApp/sequencecellrenderer.h   |   2 +-
 src/dotterApp/alignmenttool.c          |   4 +-
 src/dotterApp/dotplot.c                |   4 +-
 src/dotterApp/dotter.c                 |  18 ++---
 src/dotterApp/dotter.h                 |   6 +-
 src/dotterApp/dotterKarlin.c           |   6 +-
 src/dotterApp/dotterMain.c             |  28 +++----
 src/dotterApp/dotter_.h                |   2 +-
 src/dotterApp/greyramptool.c           |   4 +-
 src/dotterApp/seqtoolsExonView.c       |   6 +-
 src/dotterApp/seqtoolsExonView.h       |   4 +-
 src/seqtoolsUtils/blxGff3Parser.c      |   7 +-
 src/seqtoolsUtils/blxGff3Parser.h      |  51 +++++++++++-
 src/seqtoolsUtils/blxmsp.c             |  12 +--
 src/seqtoolsUtils/blxmsp.h             |   2 +-
 src/seqtoolsUtils/blxparser.c          |  10 +--
 src/seqtoolsUtils/seqtoolsWebBrowser.c | 108 +++++++++++++------------
 src/seqtoolsUtils/translate.c          |   4 +-
 src/seqtoolsUtils/utilities.c          |  23 +++---
 src/seqtoolsUtils/utilities.h          |  12 +--
 src/seqtoolsUtils/version.h            | 139 +++++++++++++++++++++++++++++++++
 39 files changed, 433 insertions(+), 299 deletions(-)

2010-11-26  Gemma Barson  <gb10@sanger.ac.uk>
 Added build scripts
 src/AUTHORS                           |    7 +
 src/COPYING                           |  674 +++++++++++++++
 src/ChangeLog                         |    0
 src/Makefile.am                       |   22 +
 src/NEWS                              |    0
 src/README                            |   72 ++
 src/blixemApp/Makefile.am             |    8 +
 src/configure.ac                      |   55 ++
 src/dotterApp/Makefile.am             |    8 +
 src/libpfetch/Makefile.am             |   29 +
 src/libpfetch/libcurlobject.c         | 1046 +++++++++++++++++++++++
 src/libpfetch/libcurlobject.h         |   80 ++
 src/libpfetch/libcurlobject_I.h       |   88 ++
 src/libpfetch/libpfetch-cmarshal.c    |  129 +++
 src/libpfetch/libpfetch-cmarshal.h    |   28 +
 src/libpfetch/libpfetch-cmarshal.list |    2 +
 src/libpfetch/libpfetch-utils.c       |  114 +++
 src/libpfetch/libpfetch.c             | 1504 +++++++++++++++++++++++++++++++++
 src/libpfetch/libpfetch.h             |  156 ++++
 src/libpfetch/libpfetch_I.h           |  239 ++++++
 src/libpfetch/libpfetch_P.h           |  125 +++
 src/seqtoolsUtils/Makefile.am         |    9 +
 22 files changed, 4395 insertions(+)

2010-11-26  Gemma Barson  <gb10@sanger.ac.uk>
 Moved source files to src subdirectory
 {blixemApp => src/blixemApp}/bigpicture.c                 | 0
 {blixemApp => src/blixemApp}/bigpicture.h                 | 0
 {blixemApp => src/blixemApp}/bigpicturegrid.c             | 0
 {blixemApp => src/blixemApp}/bigpicturegrid.h             | 0
 {blixemApp => src/blixemApp}/blixem_.h                    | 0
 {blixemApp => src/blixemApp}/blxFetch.c                   | 0
 {blixemApp => src/blixemApp}/blxdotter.c                  | 0
 {blixemApp => src/blixemApp}/blxdotter.h                  | 0
 {blixemApp => src/blixemApp}/blxmain.c                    | 0
 {blixemApp => src/blixemApp}/blxview.c                    | 0
 {blixemApp => src/blixemApp}/blxview.h                    | 0
 {blixemApp => src/blixemApp}/blxwindow.c                  | 0
 {blixemApp => src/blixemApp}/blxwindow.h                  | 0
 {blixemApp => src/blixemApp}/detailview.c                 | 0
 {blixemApp => src/blixemApp}/detailview.h                 | 0
 {blixemApp => src/blixemApp}/detailviewtree.c             | 0
 {blixemApp => src/blixemApp}/detailviewtree.h             | 0
 {blixemApp => src/blixemApp}/exonview.c                   | 0
 {blixemApp => src/blixemApp}/exonview.h                   | 0
 {blixemApp => src/blixemApp}/sequencecellrenderer.c       | 0
 {blixemApp => src/blixemApp}/sequencecellrenderer.h       | 0
 {dotterApp => src/dotterApp}/alignmenttool.c              | 0
 {dotterApp => src/dotterApp}/dotplot.c                    | 0
 {dotterApp => src/dotterApp}/dotter.c                     | 0
 {dotterApp => src/dotterApp}/dotter.h                     | 0
 {dotterApp => src/dotterApp}/dotterKarlin.c               | 0
 {dotterApp => src/dotterApp}/dotterMain.c                 | 0
 {dotterApp => src/dotterApp}/dotter_.h                    | 0
 {dotterApp => src/dotterApp}/greyramptool.c               | 0
 {dotterApp => src/dotterApp}/seqtoolsExonView.c           | 0
 {dotterApp => src/dotterApp}/seqtoolsExonView.h           | 0
 {seqtoolsUtils => src/seqtoolsUtils}/blxGff3Parser.c      | 0
 {seqtoolsUtils => src/seqtoolsUtils}/blxGff3Parser.h      | 0
 {seqtoolsUtils => src/seqtoolsUtils}/blxmsp.c             | 0
 {seqtoolsUtils => src/seqtoolsUtils}/blxmsp.h             | 0
 {seqtoolsUtils => src/seqtoolsUtils}/blxparser.c          | 0
 {seqtoolsUtils => src/seqtoolsUtils}/blxparser.h          | 0
 {seqtoolsUtils => src/seqtoolsUtils}/iupac.h              | 0
 {seqtoolsUtils => src/seqtoolsUtils}/seqtoolsWebBrowser.c | 0
 {seqtoolsUtils => src/seqtoolsUtils}/translate.c          | 0
 {seqtoolsUtils => src/seqtoolsUtils}/utilities.c          | 0
 {seqtoolsUtils => src/seqtoolsUtils}/utilities.h          | 0
 42 files changed, 0 insertions(+), 0 deletions(-)

2010-11-26  Gemma Barson  <gb10@sanger.ac.uk>
 Separated files into subdirectories
 bigpicture.c => blixemApp/bigpicture.c                     | 0
 bigpicture.h => blixemApp/bigpicture.h                     | 0
 bigpicturegrid.c => blixemApp/bigpicturegrid.c             | 0
 bigpicturegrid.h => blixemApp/bigpicturegrid.h             | 0
 blixem_.h => blixemApp/blixem_.h                           | 0
 blxFetch.c => blixemApp/blxFetch.c                         | 0
 blxdotter.c => blixemApp/blxdotter.c                       | 0
 blxdotter.h => blixemApp/blxdotter.h                       | 0
 blxmain.c => blixemApp/blxmain.c                           | 0
 blxview.c => blixemApp/blxview.c                           | 0
 blxview.h => blixemApp/blxview.h                           | 0
 blxwindow.c => blixemApp/blxwindow.c                       | 0
 blxwindow.h => blixemApp/blxwindow.h                       | 0
 detailview.c => blixemApp/detailview.c                     | 0
 detailview.h => blixemApp/detailview.h                     | 0
 detailviewtree.c => blixemApp/detailviewtree.c             | 0
 detailviewtree.h => blixemApp/detailviewtree.h             | 0
 exonview.c => blixemApp/exonview.c                         | 0
 exonview.h => blixemApp/exonview.h                         | 0
 sequencecellrenderer.c => blixemApp/sequencecellrenderer.c | 0
 sequencecellrenderer.h => blixemApp/sequencecellrenderer.h | 0
 alignmenttool.c => dotterApp/alignmenttool.c               | 0
 dotplot.c => dotterApp/dotplot.c                           | 0
 dotter.c => dotterApp/dotter.c                             | 0
 dotter.h => dotterApp/dotter.h                             | 0
 dotterKarlin.c => dotterApp/dotterKarlin.c                 | 0
 dotterMain.c => dotterApp/dotterMain.c                     | 0
 dotter_.h => dotterApp/dotter_.h                           | 0
 greyramptool.c => dotterApp/greyramptool.c                 | 0
 seqtoolsExonView.c => dotterApp/seqtoolsExonView.c         | 0
 seqtoolsExonView.h => dotterApp/seqtoolsExonView.h         | 0
 blxGff3Parser.c => seqtoolsUtils/blxGff3Parser.c           | 0
 blxGff3Parser.h => seqtoolsUtils/blxGff3Parser.h           | 0
 blxmsp.c => seqtoolsUtils/blxmsp.c                         | 0
 blxmsp.h => seqtoolsUtils/blxmsp.h                         | 0
 blxparser.c => seqtoolsUtils/blxparser.c                   | 0
 blxparser.h => seqtoolsUtils/blxparser.h                   | 0
 iupac.h => seqtoolsUtils/iupac.h                           | 0
 seqtoolsWebBrowser.c => seqtoolsUtils/seqtoolsWebBrowser.c | 0
 translate.c => seqtoolsUtils/translate.c                   | 0
 utilities.c => seqtoolsUtils/utilities.c                   | 0
 utilities.h => seqtoolsUtils/utilities.h                   | 0
 42 files changed, 0 insertions(+), 0 deletions(-)

2010-11-26  Gemma Barson  <gb10@sanger.ac.uk>
 Removed old files
 align.c     |  452 ----
 asn.c       | 2352 ----------------
 belvu.c     | 8588 -----------------------------------------------------------
 dbidx.c     |  750 ------
 diskdump.c  |  114 -
 diskfix.c   |   91 -
 efetch.c    |  533 ----
 embl.c      | 1992 --------------
 fetch.c     |  500 ----
 gfcode.c    | 1259 ---------
 hexcode.c   |  401 ---
 readseq.c   |  361 ---
 vmapdata2.c | 1895 -------------
 vmapphys.c  |  417 ---
 14 files changed, 19705 deletions(-)

2010-11-18  gb10  <gb10>
 Added help for new features
 blxwindow.c | 275 +++++++++++++++++++++++++++++++-----------------------------
 dotter.c    |  25 +++++-
 2 files changed, 162 insertions(+), 138 deletions(-)

2010-11-17  gb10  <gb10>
 Fixed reading frame calculation for reverse strand. Fixed a bug where polya signals were not being shown. Fixed a bug where CDS/UTRs were not being shown in the correct tree.
 blxwindow.c            | 14 +++++---
 detailview.c           | 55 ++++++-------------------------
 detailviewtree.c       |  2 +-
 sequencecellrenderer.c | 19 +++++------
 utilities.c            | 87 +++++++++++++++++++++++++++++++++-----------------
 5 files changed, 87 insertions(+), 90 deletions(-)

2010-11-16  gb10  <gb10>
 Fixed an incorrect error message
 dotter.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

2010-11-16  gb10  <gb10>
 Improved message handlingwd
 dotterMain.c | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

2010-11-16  gb10  <gb10>
 Improved message handling
 blxmain.c    |  9 +++++----
 blxwindow.c  |  2 +-
 dotter.c     | 10 +++++++++-
 dotterMain.c | 13 ++++++++-----
 utilities.c  | 56 +++++++++++++++++++++++---------------------------------
 5 files changed, 46 insertions(+), 44 deletions(-)

2010-11-16  gb10  <gb10>
 Removed ACEDB compile option. Fixed a bug with piping X options from blixem to dotter. Improved message handling.wd
 utilities.c | 4 ++++
 1 file changed, 4 insertions(+)

2010-11-16  gb10  <gb10>
 Removed ACEDB compile option. Fixed a bug with piping X options from blixem to dotter. Improved message handling.
 blixem_.h          |  26 +--
 blxFetch.c         |  34 +--
 blxdotter.c        | 159 +++++++------
 blxmsp.c           | 368 +++++++++++++++++++++++------
 blxmsp.h           |  19 +-
 blxparser.c        |  18 +-
 blxview.c          | 669 +----------------------------------------------------
 blxwindow.c        |  21 +-
 detailview.c       |  41 ++++
 detailviewtree.c   |   5 -
 dotplot.c          |  12 +-
 dotter.c           |  41 ++--
 dotter.h           |  37 +--
 dotterKarlin.c     |  22 +-
 dotterMain.c       | 178 +++++++++-----
 seqtoolsExonView.c |   7 -
 utilities.c        | 480 +++++++++++++++++++++++++++++++++++++-
 utilities.h        |  16 +-
 18 files changed, 1125 insertions(+), 1028 deletions(-)

2010-11-15  gb10  <gb10>
 Added percentID tag in GFF parser
 blxGff3Parser.c | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

2010-11-11  gb10  <gb10>
 Fixed a potential crash where an incorrect frame could be returned for nucleotide matches
 detailview.c | 43 +------------------------------------------
 1 file changed, 1 insertion(+), 42 deletions(-)

2010-11-11  gb10  <gb10>
 Fixed a warning message that was too long
 blxdotter.c | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

2010-11-11  gb10  <gb10>
 Fixed a bug where the reference sequence was being offset incorrectly when the display is at the end of the reference sequence range
 detailviewtree.c | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

2010-11-11  gb10  <gb10>
 Fixed a bug where protein gap coords were being messed up because blast mode wasn't being set
 blxmain.c | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

2010-11-09  gb10  <gb10>
 Improved warnings when calling dotter with a bad range
 blxdotter.c | 92 ++++++++++++++++++++++++++++++++++++-------------------------
 1 file changed, 55 insertions(+), 37 deletions(-)

2010-11-09  gb10  <gb10>
 Fixed a small bug where the preview box was not being positioned accurately when the display is reversed
 bigpicture.c     | 20 ++++++++++++--------
 bigpicturegrid.c |  3 ++-
 2 files changed, 14 insertions(+), 9 deletions(-)

2010-11-09  gb10  <gb10>
 Fixed a bug with resizing columns
 detailview.c     | 30 ++----------------------------
 detailview.h     |  2 +-
 detailviewtree.c | 54 +++++++++++++++++++++++++-----------------------------
 detailviewtree.h |  1 +
 4 files changed, 29 insertions(+), 58 deletions(-)

2010-11-09  gb10  <gb10>
 Fixed a bug with long options. Fixed a bug with the highlight-diffs argument
 blixem_.h   |  4 ++--
 blxmain.c   | 12 +++++++++---
 blxwindow.c |  1 +
 3 files changed, 12 insertions(+), 5 deletions(-)

2010-11-08  gb10  <gb10>
 Made some improvements to the key file (can now pass separate colors for UTR and CDS regions of the same source)
 blxmain.c   | 28 +++++++++---------
 blxmsp.c    | 14 ++++++---
 blxview.c   | 96 ++++++++++++++++++++++++++++++++++---------------------------
 utilities.h |  2 ++
 4 files changed, 81 insertions(+), 59 deletions(-)

2010-11-08  gb10  <gb10>
 Implemented the reverse-strand command-line argument
 blxwindow.c | 5 +++++
 1 file changed, 5 insertions(+)

2010-11-08  gb10  <gb10>
 Implemented negate-coords option
 bigpicture.c     |  4 ++++
 blxwindow.c      | 10 ++++++++++
 blxwindow.h      |  1 +
 detailview.c     | 53 ++++++++++-------------------------------------------
 detailviewtree.c | 20 ++++++++++++++++++--
 5 files changed, 43 insertions(+), 45 deletions(-)

2010-11-08  gb10  <gb10>
 Changed blixem command-line arguments. Added long options.wd
 blixem_.h   |  4 +++-
 blxmain.c   | 33 ++++++++++++++++++++++++++++++---
 blxwindow.c |  1 +
 3 files changed, 34 insertions(+), 4 deletions(-)

2010-11-08  gb10  <gb10>
 Changed blixem command-line arguments. Added long options.
 blixem_.h              |  56 +++++-
 blxGff3Parser.c        |  81 +++------
 blxGff3Parser.h        |   5 +-
 blxdotter.c            |  24 +--
 blxdotter.h            |   1 -
 blxmain.c              | 456 ++++++++++++++++++++++++++++++++++---------------
 blxparser.c            | 224 ++++++++++--------------
 blxparser.h            |   2 +-
 blxview.c              | 200 ++++++----------------
 blxview.h              |  48 +-----
 blxwindow.c            |  24 ++-
 blxwindow.h            |  32 ----
 dotter.c               |  27 +--
 dotter.h               |   5 +-
 dotterMain.c           |  20 +--
 sequencecellrenderer.h |   2 +-
 16 files changed, 573 insertions(+), 634 deletions(-)

2010-11-05  gb10  <gb10>
 For GFF3, get percent ID from parsed tag
 blixem_.h       |  4 ++--
 blxGff3Parser.c | 22 +++++++++++++++++++---
 blxparser.c     | 14 +++++++-------
 blxview.c       |  8 +++++---
 blxwindow.c     |  6 +++---
 5 files changed, 36 insertions(+), 18 deletions(-)

2010-11-05  gb10  <gb10>
 Fixed a potential memory bug when starting dotter
 blxdotter.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-11-04  gb10  <gb10>
 Use start coord as centre of display rather than left edge
 blxmain.c    |  6 +++---
 detailview.c | 11 ++++++-----
 2 files changed, 9 insertions(+), 8 deletions(-)

2010-11-03  gb10  <gb10>
 More removal of acedb code
 blxFetch.c         |   3 +-
 blxselect.c        | 501 -----------------------------------------------------
 exonview.h         |   2 +-
 seqtoolsExonView.h |   2 +-
 4 files changed, 4 insertions(+), 504 deletions(-)

2010-11-03  gb10  <gb10>
 Removed more acedb code from dotter
 blxFetch.c  | 51 +++++++++++++++++++++++++++------------------------
 blxdotter.c |  6 +++---
 blxmain.c   | 48 ++++++++++++++++++++++++++----------------------
 blxparser.c | 26 ++++++++++++++++++++++++--
 blxview.c   |  9 ++-------
 dotplot.c   | 53 ++++++++++++-----------------------------------------
 translate.c | 16 ++++++++--------
 utilities.c | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 utilities.h | 15 +++++++++++++++
 9 files changed, 176 insertions(+), 107 deletions(-)

2010-11-03  gb10  <gb10>
 Fixed a regression where dotter was failing to start because of a programming error (invalid pointer passed to getFontCharSize). Removed some more acedb code from dotter.
 alignmenttool.c |  41 +++++++++----------
 blixem_.h       |   9 +----
 blxview.c       |   6 ++-
 dotplot.c       |  17 +++++++-
 dotter.c        | 119 +++++++++++---------------------------------------------
 dotterMain.c    |   8 ++--
 dotter_.h       |   6 +--
 utilities.c     |  83 ++++++++++++++++++++++++++++++++++++++-
 utilities.h     |   3 ++
 9 files changed, 156 insertions(+), 136 deletions(-)

2010-11-02  gb10  <gb10>
 Added parsing of a sequence-region comment line for exblx and seqbl file formats. Use the parsed range as the reference sequence range in blixem (i.e. if a ref seq range is passed, all feature coords in the file must be in that range; otherwise, coords are assumed to be 1-based). Note that if an offset is supplied via the -O argument, the offset will be applied on top of this, i.e. both the ref seq range and all feature coords will be offset.
 blxmain.c   |  4 ++--
 blxparser.c | 31 ++++++++++++++++++++++++-------
 blxview.c   |  5 +++--
 blxview.h   |  3 ++-
 blxwindow.c | 13 ++++++-------
 blxwindow.h |  3 ++-
 6 files changed, 39 insertions(+), 20 deletions(-)

2010-11-02  gb10  <gb10>
 Check that parsed sequence range is the same length as the FASTA sequence
 blxparser.c | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

2010-11-02  gb10  <gb10>
 Set a default ref seq range if none was parsed
 blxparser.c | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

2010-11-02  gb10  <gb10>
 GFF3 parser now reads reference sequence range from file.
 blxGff3Parser.c |  8 ++++----
 blxGff3Parser.h |  3 ++-
 blxmain.c       |  7 ++++---
 blxparser.c     | 13 +++++++------
 blxparser.h     |  2 +-
 blxselect.c     |  6 ++++--
 detailview.c    |  2 +-
 dotterMain.c    |  5 +++--
 8 files changed, 26 insertions(+), 20 deletions(-)

2010-11-02  gb10  <gb10>
 Made detail-view alignment positions more accurate if characters are not an exact number of pixels wide
 bigpicture.c           |  4 +--
 bigpicture.h           |  4 +--
 bigpicturegrid.c       |  6 ++--
 blxFetch.c             |  4 +--
 blxwindow.c            |  4 +--
 detailview.c           | 54 +++++++++++++++----------------
 detailview.h           | 10 +++---
 detailviewtree.c       | 16 +++++-----
 exonview.c             |  2 +-
 sequencecellrenderer.c | 87 ++++++++++++++++++++++++++++++++------------------
 utilities.c            |  7 ++--
 utilities.h            |  2 +-
 12 files changed, 113 insertions(+), 87 deletions(-)

2010-11-01  gb10  <gb10>
 Make tree widgets use same font description as detail view
 detailview.c | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

2010-11-01  gb10  <gb10>
 Improved blixem responsiveness when variation and polyA data is included
 blixem_.h              |  53 +++++++++-
 blxGff3Parser.c        |   7 +-
 blxGff3Parser.h        |   1 +
 blxmain.c              |  14 ++-
 blxmsp.c               | 243 +++++----------------------------------------
 blxmsp.h               |  34 +------
 blxparser.c            |  88 ++++++++++-------
 blxparser.h            |   2 +-
 blxselect.c            |  10 +-
 blxview.c              | 231 ++++++++++++++++++++++++++++++++++++++++---
 blxview.h              |   3 +-
 blxwindow.c            |  88 ++++++++---------
 blxwindow.h            |   5 +-
 detailview.c           | 264 ++++++++++++++++++++++++++++++++-----------------
 detailview.h           |   7 +-
 detailviewtree.c       |  69 ++++++-------
 dotterMain.c           |  17 +++-
 sequencecellrenderer.c |   6 +-
 utilities.c            |   7 +-
 utilities.h            |  25 -----
 20 files changed, 655 insertions(+), 519 deletions(-)

2010-11-01  gb10  <gb10>
 Improved use of font selection dialog
 blxFetch.c  |  4 +--
 blxwindow.c | 81 ++++++++++++++++++++++++++++++++++++-------------------------
 2 files changed, 50 insertions(+), 35 deletions(-)

2010-11-01  gb10  <gb10>
 Fix for RT ticket 165740: fixed-width fonts were not displaying properly on certain machines. Also added a font selection option in the Settings dialog.
 blxwindow.c  | 84 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++---
 detailview.c |  3 ++-
 2 files changed, 82 insertions(+), 5 deletions(-)

2010-10-28  gb10  <gb10>
 Fixed a bug where sorting by ID is ambiguous if the IDs are within 1 of each other
 detailviewtree.c | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

2010-10-28  gb10  <gb10>
 Fixed a bug in dotter where HSP lines were drawn in the wrong place when the display is reversed
 dotplot.c | 186 ++++++++++++++++----------------------------------------------
 1 file changed, 48 insertions(+), 138 deletions(-)

2010-10-28  gb10  <gb10>
 Fixed a bug in dotter where the dotplot was not always initialised correctly
 dotplot.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2010-10-28  gb10  <gb10>
 Fixed a bug where the calculated dotter range was being clipped too much for a large object. Added a warning if the clipped range no longer contains any matches. Blixem now calls dotter as an external process and kills all spawned dotters on exit. Fixed a bug with drawing HSP lines in dotter where they were being drawn in the wrong place if they extend outside the visible range.
 blxdotter.c  | 223 ++++++++++++++++++++++++++++++++++++++++++++---------------
 blxmsp.c     |   2 +-
 blxwindow.c  |  22 ++++++
 blxwindow.h  |   1 +
 dotplot.c    |  33 +++++++--
 dotter.c     | 209 ++++++++++++++++++++++++++++++++++++++++++-------------
 dotterMain.c |  31 ++++++---
 utilities.h  |   2 -
 8 files changed, 401 insertions(+), 122 deletions(-)

2010-10-26  gb10  <gb10>
 Fixed a typo
 dotplot.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-10-26  gb10  <gb10>
 Fixed a bug where MSPs were not being passed from blixem to dotter
 blxdotter.c        |  23 +----
 blxmsp.c           | 268 ++++++++++++++++++++++++++++++++++++++++++++++++-----
 blxmsp.h           |  10 +-
 blxview.c          |  86 +----------------
 blxwindow.c        |   8 --
 detailview.c       |   2 +-
 dotplot.c          |  10 +-
 dotter.c           |   4 +-
 dotterMain.c       | 100 +++++++++-----------
 seqtoolsExonView.c |   9 +-
 utilities.h        |   2 +
 11 files changed, 324 insertions(+), 198 deletions(-)

2010-10-26  gb10  <gb10>
 Added -H option when calling dotter externally from blixem)
 blxdotter.c | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

2010-10-26  gb10  <gb10>
 Call dotter as an external process from blixem
 blxdotter.c  | 224 ++++++++++++++++++++++++++++++++++++-------
 dotter.c     | 305 +++++++++++------------------------------------------------
 dotter.h     |  48 ++++++++--
 dotterMain.c | 174 ++++++++++++----------------------
 utilities.c  |  68 +++++++++++++
 utilities.h  |   2 +
 6 files changed, 412 insertions(+), 409 deletions(-)

2010-10-26  gb10  <gb10>
 Fixed a bug when calling dotter in HSP-only mode
 alignmenttool.c |  2 +-
 dotplot.c       |  3 ++-
 dotter.c        | 39 +++++++++++++++------------------------
 dotter_.h       |  4 ++--
 4 files changed, 20 insertions(+), 28 deletions(-)

2010-10-25  gb10  <gb10>
 Fixed a bug in the new dotter where artefacts were appearing in the dot-plot for protein matches. This was because the sum arrays were not being cleared between the calculations for each frame. Also fixed a bug where HSPs were shown the wrong way round when the display is reversed.
 dotplot.c | 91 ++++++++++++++++++++++++++++++---------------------------------
 1 file changed, 43 insertions(+), 48 deletions(-)

2010-10-25  gb10  <gb10>
 Consolidated more dotter code
 dotplot.c | 511 +++++++++++++++++++++++++++++---------------------------------
 1 file changed, 239 insertions(+), 272 deletions(-)

2010-10-25  gb10  <gb10>
 Consolidated some duplicated dotter code
 dotplot.c | 308 ++++++++++++++++++++++++++++++++------------------------------
 1 file changed, 157 insertions(+), 151 deletions(-)

2010-10-22  gb10  <gb10>
 Changed to new, GTK-based dotter
 blxparser.c      | 108 +++----------------------------------------------------
 detailviewtree.c |  75 +++++++++++++++++++++++++-------------
 2 files changed, 54 insertions(+), 129 deletions(-)

2010-10-22  gb10  <gb10>
 Changed to new, GTK-based dotter
 alignmenttool.c                     |  912 +++++
 bigpicture.c                        |   72 +-
 bigpicture.h                        |    9 -
 bigpicturegrid.c                    |   20 +-
 blixem_.h                           |  113 +-
 blxFetch.c                          |   26 +-
 blxGff3Parser.c                     |    3 +-
 blxGff3Parser_.h => blxGff3Parser.h |    7 +-
 blxdotter.c                         |  158 +-
 blxmain.c                           |    4 +-
 blxmsp.c                            | 1156 +++++++
 blxmsp.h                            |  274 ++
 blxparser.h                         |   15 +
 blxselect.c                         |    3 +-
 blxview.c                           |   69 +-
 blxview.h                           |  215 +-
 blxwindow.c                         |  518 +--
 blxwindow.h                         |   16 -
 detailview.c                        |  367 +-
 dotplot.c                           | 2646 +++++++++++++++
 dotter.c                            | 6242 +++++++++++++++--------------------
 dotter.h                            |   13 +-
 dotterKarlin.c                      |   16 +-
 dotterMain.c                        |   43 +-
 dotter_.h                           |  232 +-
 exonview.c                          |   35 +-
 exonview.h                          |    7 +-
 greyramptool.c                      |  791 +++++
 seqtoolsExonView.c                  |  642 ++++
 seqtoolsExonView.h                  |   43 +
 sequencecellrenderer.c              |   28 +-
 translate.c                         |    4 +-
 utilities.c                         | 1815 ++++------
 utilities.h                         |  232 +-
 34 files changed, 10789 insertions(+), 5957 deletions(-)

2010-10-19  gb10  <gb10>
 Use reading frame from file for exblx file format rather than calculating it
 blxview.c   |  6 +-----
 blxwindow.c | 14 ++++++++++++--
 2 files changed, 13 insertions(+), 7 deletions(-)

2010-10-19  gb10  <gb10>
 Fixed a regression where the reading frame was being calculated incorrectly
 blxparser.c | 14 +++++++-------
 blxview.c   |  8 ++++----
 2 files changed, 11 insertions(+), 11 deletions(-)

2010-10-18  gb10  <gb10>
 Added code to unescape the URL tag that is passed in the GFF file for variations
 blxGff3Parser.c | 30 ++++--------------------------
 blxview.c       |  8 +++++++-
 2 files changed, 11 insertions(+), 27 deletions(-)

2010-10-18  gb10  <gb10>
 Added variant_sequence to parsed tags
 blxGff3Parser.c | 4 ++++
 1 file changed, 4 insertions(+)

2010-10-18  gb10  <gb10>
 Fixed a bug with calculating the reading frame for CDSs on the reverse strand. Also removed some unnecessary warnings from the gff3 parser
 blxGff3Parser.c |  4 +++-
 blxwindow.c     | 49 +++++++++++++++++------------------------
 utilities.c     | 68 ++++++++++++++++++++++++++++++---------------------------
 3 files changed, 59 insertions(+), 62 deletions(-)

2010-10-08  gb10  <gb10>
 Fixed a couple of potential memory bugs
 blxdotter.c | 17 +++++++++++++++++
 blxwindow.c |  7 +++++--
 2 files changed, 22 insertions(+), 2 deletions(-)

2010-10-06  gb10  <gb10>
 Renamed the 'GSettings' function to avoid a clash with Glib (glib2 port, version 2.26.0_0)
 detailview.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2010-10-06  gb10  <gb10>
 Double-click a variation to open its URL
 blxGff3Parser.c      |  26 +++++++++++
 detailview.c         | 103 +++++++++++++++++++++++++++++--------------
 detailview.h         |  11 +++++
 detailviewtree.c     | 120 +++++++++++++++++++++++++++++++++++++++++++--------
 seqtoolsWebBrowser.c |   6 +--
 utilities.c          |   5 +++
 utilities.h          |   4 +-
 7 files changed, 221 insertions(+), 54 deletions(-)

2010-10-06  gb10  <gb10>
 Added better code for calling a web browser and used this for pfetch-www mode
 blixem_.h            |   3 +-
 blxFetch.c           | 238 ++++++++++++++++---------------
 seqtoolsWebBrowser.c | 387 +++++++++++++++++++++++++++++++++++++++++++++++++++
 utilities.h          |   6 +-
 4 files changed, 516 insertions(+), 118 deletions(-)

2010-10-05  gb10  <gb10>
 Added parsing of URL for variations. Added variation alternatives to feedback box when user clicks on a variation
 blixem_.h       |  4 ++--
 blxGff3Parser.c | 16 +++++++++++-----
 blxparser.c     | 14 +++++++-------
 blxview.c       |  9 ++++++---
 blxview.h       |  3 ++-
 detailview.c    |  9 +++++++--
 6 files changed, 35 insertions(+), 20 deletions(-)

2010-10-05  gb10  <gb10>
 Fixed a small bug with SNP positioning
 detailview.c | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

2010-10-05  gb10  <gb10>
 Added copy_number_variation type
 blxGff3Parser.c | 1 +
 1 file changed, 1 insertion(+)

2010-10-05  gb10  <gb10>
 Added support for zero-length variations. Also we now only highlight a base in orange if it is part of a selected variation (before it used to highlight if the base index was selected).
 blxwindow.c  |  18 +++++++----
 blxwindow.h  |   2 ++
 detailview.c | 101 ++++++++++++++++++++++++++++++++++++++++++++++++-----------
 3 files changed, 97 insertions(+), 24 deletions(-)

2010-10-05  gb10  <gb10>
 Fixed a regression where grid labels weren't being displayed when the display is reversed
 bigpicture.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-10-05  gb10  <gb10>
 Added a type for BlxSequence
 blxFetch.c  | 14 +++++------
 blxparser.c |  6 ++---
 blxview.c   | 78 +++++++++++++++++++++++++++++++++++++------------------------
 blxview.h   | 20 ++++++++++++----
 utilities.c | 18 +++++++++++---
 utilities.h |  2 ++
 6 files changed, 91 insertions(+), 47 deletions(-)

2010-10-05  gb10  <gb10>
 Added support for variations
 blxFetch.c      |   8 +--
 blxGff3Parser.c |   8 ++-
 blxview.c       |  31 +++++------
 blxview.h       |   9 ++--
 detailview.c    | 158 ++++++++++++++++++++++++++++----------------------------
 utilities.c     |  21 ++++++--
 utilities.h     |   4 +-
 7 files changed, 132 insertions(+), 107 deletions(-)

2010-10-05  gb10  <gb10>
 Fixed a bug with drawing clipped intron lines
 exonview.c | 29 ++++++++++++++---------------
 1 file changed, 14 insertions(+), 15 deletions(-)

2010-10-04  gb10  <gb10>
 Fixed a bug where introns were being drawn with more acute angles if the end goes out of the edge of the view
 bigpicturegrid.c |  2 +-
 exonview.c       | 69 +++++++++++++++++++++++++++-----------------------------
 2 files changed, 34 insertions(+), 37 deletions(-)

2010-10-04  gb10  <gb10>
 Changed the big picture to show coords on a per-nucleotide basis rather than per-peptide, which fixes a bug where there were sometimes gaps between adjacent exons and introns.
 exonview.c | 121 ++++++++++++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 92 insertions(+), 29 deletions(-)

2010-10-04  gb10  <gb10>
 Changed the big picture to show coords on a per-nucleotide basis rather than per-peptide, which fixes a bug where there were sometimes gaps between adjacent exons and introns.
 bigpicture.c     | 100 +++++++++++++++++++++++++++++++----------------
 bigpicture.h     |   8 ++--
 bigpicturegrid.c |  50 ++++++++++++++----------
 exonview.c       | 116 +++++++++++++++++++++++++++++++++++++++----------------
 utilities.c      |  14 +++++++
 utilities.h      |   7 ++++
 6 files changed, 204 insertions(+), 91 deletions(-)

2010-09-30  gb10  <gb10>
 Fixed a bug where the exon view was not displaying exons that span more than the width of the view
 exonview.c | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

2010-09-30  gb10  <gb10>
 Fixed an off-by-one error when calculating intron start/end positions
 blxview.c  | 6 +++---
 exonview.c | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

2010-09-30  gb10  <gb10>
 Fixed a bug with middle-dragging on the exon view when caps lock is on
 exonview.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-09-30  gb10  <gb10>
 Fixed some bugs with calculating introns and sorting by position on the reverse strand
 blxview.c        |  4 ++--
 detailview.c     |  4 +++-
 detailviewtree.c | 45 ++++++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 49 insertions(+), 4 deletions(-)

2010-09-30  gb10  <gb10>
 Fixed a bug where CDS/UTR boundaries were calculated incorrectly for exons on the reverse strand. Also fixed a bug where exon view was not redrawing on window resize
 bigpicture.c           |  6 ++++++
 blxview.c              | 50 ++++++++++++++++++++++++++++++++++++++++++--------
 blxview.h              |  7 ++++---
 detailview.c           |  2 +-
 detailviewtree.c       | 13 +++++++++++--
 sequencecellrenderer.c |  2 +-
 6 files changed, 65 insertions(+), 15 deletions(-)

2010-09-29  gb10  <gb10>
 Made the big picture scrollable, which fixes some issues where the big picture section can get too large when exons are bumped or the grid scale is changed
 bigpicture.c | 113 +++++++++++++++++++++++++++++--------
 bigpicture.h |   2 +-
 blxwindow.c  |  47 +++++++++++++++-
 detailview.c | 179 ++++++++++++++++++++++++++++-------------------------------
 detailview.h |   2 +-
 exonview.c   |   5 ++
 utilities.c  |  26 +++++++++
 utilities.h  |   2 +
 8 files changed, 255 insertions(+), 121 deletions(-)

2010-09-28  gb10  <gb10>
 Added polyA signal highlighting in the reference sequence
 detailview.c | 96 +++++++++++++++++++++++++++++++++++++++++++++++++++++++-----
 utilities.c  | 37 +++++++++++++----------
 utilities.h  |  1 +
 3 files changed, 111 insertions(+), 23 deletions(-)

2010-09-28  gb10  <gb10>
 Added flag for highlighting polyA signals in the reference sequence. Made higlighting of special bases in the reference sequence more generic
 blxwindow.c            | 37 +++++++++++++---------
 detailview.c           | 83 +++++++++++++++++++++++---------------------------
 detailview.h           | 11 +------
 detailviewtree.c       |  4 +--
 sequencecellrenderer.c |  4 +--
 utilities.c            |  4 +--
 utilities.h            |  6 ++--
 7 files changed, 71 insertions(+), 78 deletions(-)

2010-09-28  gb10  <gb10>
 Fixed a bug with drawing exons introduced in previous changes
 sequencecellrenderer.c |  2 +-
 utilities.c            | 22 +++++++++++++++-------
 utilities.h            |  2 +-
 3 files changed, 17 insertions(+), 9 deletions(-)

2010-09-27  gb10  <gb10>
 Highlight polyA tails in red
 sequencecellrenderer.c | 19 +++++++++++++++----
 utilities.c            | 14 ++++++++++++++
 utilities.h            |  1 +
 3 files changed, 30 insertions(+), 4 deletions(-)

2010-09-27  gb10  <gb10>
 Can now view polyA tails
 blxGff3Parser.c        |  14 +++--
 blxview.c              |   9 ++-
 blxwindow.c            | 165 +++++++++++++++++++++++++++----------------------
 blxwindow.h            |  24 +------
 detailview.c           |  22 +++----
 detailview.h           |   1 -
 detailviewtree.c       |  11 ++--
 sequencecellrenderer.c |  13 ++--
 utilities.c            |  86 ++++++++++++++++++++++----
 utilities.h            |  50 +++++++++++++--
 10 files changed, 244 insertions(+), 151 deletions(-)

2010-09-27  gb10  <gb10>
 Added poly_site and polya_signal_sequence GFF types. Consolidated some code that calculates the full display range of an MSP including any unaligned portions of the match sequence
 blxGff3Parser.c        |   2 +-
 blxview.c              |   4 +-
 blxview.h              |   4 +-
 detailview.c           |   7 +--
 detailviewtree.c       | 111 +++++------------------------------
 sequencecellrenderer.c |  79 ++++++-------------------
 utilities.c            | 153 ++++++++++++++++++++++++++++++++++++++-----------
 utilities.h            |   7 ++-
 8 files changed, 164 insertions(+), 203 deletions(-)

2010-09-27  gb10  <gb10>
 Fixed a few bugs with gff input
 blxGff3Parser.c | 24 +++++++++++++++++++-----
 blxview.c       | 42 +++++++++++++++++++++++++-----------------
 blxview.h       |  5 +++--
 utilities.c     |  2 +-
 utilities.h     |  2 +-
 5 files changed, 49 insertions(+), 26 deletions(-)

2010-09-21  gb10  <gb10>
 Fixed a bug where pfetch was being called multiple times when starting dotter. Changed the client name sent to pfetch from 'acedb' to the application name
 blxFetch.c   |  6 +++---
 blxdotter.c  | 55 +++++++++++++++++++++++++++++++------------------------
 blxdotter.h  |  3 ++-
 blxview.c    | 10 ++++++++--
 blxwindow.c  |  2 +-
 detailview.c |  2 +-
 6 files changed, 46 insertions(+), 32 deletions(-)

2010-09-06  gb10  <gb10>
 Fixed a bug with getting dotter coords from the current big-picture display range in protein blixem
 blxdotter.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

2010-09-03  gb10  <gb10>
 Added bounds-checking on manual dotter coords. Changed several dialogs so that they are not closed if there is an error with the data entered.
 bigpicture.c |  18 ++++++--
 bigpicture.h |   6 +--
 blxFetch.c   |   6 ++-
 blxdotter.c  |  91 ++++++++++++++++++++++++++++++----------
 blxview.c    |  12 +++---
 blxwindow.c  | 135 +++++++++++++++++++++++++++++++++++++++++++++--------------
 utilities.c  |  40 ++++++++++++++----
 utilities.h  |   6 +--
 8 files changed, 237 insertions(+), 77 deletions(-)

2010-08-31  gb10  <gb10>
 Removed some redundant code from dotter
 dotter.c     | 44 +++-----------------------------------------
 dotterMain.c |  7 +------
 2 files changed, 4 insertions(+), 47 deletions(-)

2010-08-31  gb10  <gb10>
 Replaced messcrash with g_error
 dotter.c       |  8 +++++---
 dotterKarlin.c |  7 ++-----
 dotterMain.c   | 21 ++++++++-------------
 3 files changed, 15 insertions(+), 21 deletions(-)

2010-08-31  gb10  <gb10>
 Dotter: replaced messalloc/messfree by g_malloc/g_free. Removed some unused items from dotter_.h and removed use of dotter_.h from belvu because it doesn't seem to contain anything that is being used.
 belvu.c        |   4 +-
 blxdotter.c    |  46 +++++++++-------------
 dotter.c       | 122 ++++++++++++++++++++++++++-------------------------------
 dotter.h       |  10 ++---
 dotterKarlin.c |  46 +++++++++++-----------
 dotterMain.c   |  85 ++++++++++++++++++++++------------------
 dotter_.h      |  27 ++-----------
 7 files changed, 151 insertions(+), 189 deletions(-)

2010-08-31  gb10  <gb10>
 Small error-checking improvements
 blxGff3Parser.c | 2 +-
 blxwindow.c     | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

2010-08-31  gb10  <gb10>
 Added a prefix to the 'organism' data field so that a narrow column width can be used that displays just the prefix
 blxview.c | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 55 insertions(+), 2 deletions(-)

2010-08-27  gb10  <gb10>
 Fixed some GTK warnings that happen if all of the detail-view panes are hidden
 detailview.c     | 16 ++++++++++------
 detailviewtree.c |  2 +-
 2 files changed, 11 insertions(+), 7 deletions(-)

2010-08-27  gb10  <gb10>
 Fixed a couple of bugs with squash matches: go-to-next was highlighting the wrong frame for protein matches; MSPs for both strands were being added to each tree.
 detailview.c     | 15 ++++++---------
 detailviewtree.c | 56 ++++++++++++++++++++++++++++++++------------------------
 2 files changed, 38 insertions(+), 33 deletions(-)

2010-08-27  gb10  <gb10>
 Removed the need for the -F command line option when a single input file is used. If blixem is called with one input file, it is assumed to contain both alignment data and the reference sequence. If it is called with two files, the first is assumed to contain the reference sequence and the second the alignment data. The -F option has been left in for now for backwards compatibility.
 blxmain.c | 27 +++++++++++++++------------
 1 file changed, 15 insertions(+), 12 deletions(-)

2010-08-27  gb10  <gb10>
 Fixed a couple of bugs with the GFF parser: sequence name was not being read from the header; fixed a problem with constructing introns
 blxGff3Parser.c |  38 +++++++++---------
 blxparser.c     |   9 ++---
 blxview.c       | 118 +++++++++++++++++++++++++++++++++-----------------------
 blxview.h       |   4 +-
 4 files changed, 95 insertions(+), 74 deletions(-)

2010-08-26  gb10  <gb10>
 Fixed a bug in the GFF parser to allow consecutive I and D's in CIGAR string
 blxGff3Parser.c | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

2010-08-26  gb10  <gb10>
 Added range checking for big picture scale
 bigpicture.c | 56 +++++++++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 49 insertions(+), 7 deletions(-)

2010-08-26  gb10  <gb10>
 A few improvements to GFF parsing
 blxGff3Parser.c | 37 ++++++++++++++++++++-----------
 blxview.c       | 14 +++++++++---
 blxwindow.c     | 69 ++++++++++++++++++++++++++++++---------------------------
 3 files changed, 71 insertions(+), 49 deletions(-)

2010-08-26  gb10  <gb10>
 Updated blixem version and help
 blixem_.h   |  4 ++--
 blxwindow.c | 31 +++++++++++++++++--------------
 2 files changed, 19 insertions(+), 16 deletions(-)

2010-08-26  gb10  <gb10>
 Fixed a bug with the detail-view statusbar when 'squash matches' is enabled
 detailviewtree.c | 25 +++++++++++++------------
 utilities.c      | 32 ++++++++++++++++++++------------
 utilities.h      |  2 +-
 3 files changed, 34 insertions(+), 25 deletions(-)

2010-08-26  gb10  <gb10>
 Added two status bars: one for messages and one for feeding back info about the currently moused-over item. Fixed a bug with parsing peptide sequence data from seqbl files. Fixed some bugs with negative offset: some termini were being shown as splice sites; go-to-next match was sometimes messing up.
 blixem_.h              |   5 +-
 blxFetch.c             |  53 +-----
 blxdotter.c            |   8 +-
 blxparser.c            |  65 +++++--
 blxview.c              | 463 ++++++++++++++++++++++++++++++++++++++++++++++---
 blxwindow.c            |  36 ++--
 blxwindow.h            |   2 +
 detailview.c           |  53 ++++--
 detailview.h           |   1 +
 detailviewtree.c       | 119 ++++++++++++-
 sequencecellrenderer.c |  19 +-
 utilities.c            | 443 +++++++++++-----------------------------------
 utilities.h            |   9 +-
 13 files changed, 789 insertions(+), 487 deletions(-)

2010-08-24  gb10  <gb10>
 Parse actual name out of Gene Name field rather than including the whole line
 blixem_.h   |   3 +-
 blxparser.c |   5 +-
 blxview.c   | 288 +++++++++++++++++++++++++++++++++---------------------------
 3 files changed, 161 insertions(+), 135 deletions(-)

2010-08-24  gb10  <gb10>
 Added support for grouping exons by parent transcript ID (i.e. as passed in GFF format). Added full support for CDS/UTR types. Calculate the reading frame, using the given phase, if applicable. Changed score and ID to be decimal values rather than integers and allow grid scale to show fractions of an integer per cell. Reduced exon size and padding when the exon view is bumped. Added GT-AG to list of canonical splice sites. Removed incorrect splice-site highlighting which was being shown at the termini.
 bigpicture.c           |  27 ++--
 bigpicture.h           |  16 +--
 bigpicturegrid.c       |  32 +++--
 bigpicturegrid.h       |   2 +-
 blixem_.h              |  18 +--
 blxGff3Parser.c        | 346 ++++++++++++++++++++++++--------------------
 blxdotter.c            |   4 +-
 blxparser.c            |  40 +++---
 blxview.c              | 380 +++++++++++++++++++++++++++++++++++++++++++++----
 blxview.h              |  75 +++++-----
 blxwindow.c            | 177 +++++++++++++++--------
 blxwindow.h            |   3 +-
 detailview.c           |  22 +--
 detailviewtree.c       |  87 +++++++----
 dotter.c               |  75 +++++-----
 dotter.h               |   4 +-
 dotterMain.c           |   6 +-
 exonview.c             |  28 +++-
 sequencecellrenderer.c |  81 +++++++----
 utilities.c            | 216 ++++++++++++++++++++--------
 utilities.h            |  13 +-
 21 files changed, 1138 insertions(+), 514 deletions(-)

2010-08-17  gb10  <gb10>
 Fixed a bug where blixem was quitting if pfetch returned 'no match' on startup
 blxFetch.c | 33 +++++++++++++--------------------
 1 file changed, 13 insertions(+), 20 deletions(-)

2010-08-16  gb10  <gb10>
 Fixed some bugs with GFF parser
 blxFetch.c  |  9 ++----
 blxparser.c | 70 ++++++++++++++++++++++++++++++-------------
 blxview.c   | 99 ++++++++++++++++++++++++++++++++++++-------------------------
 3 files changed, 109 insertions(+), 69 deletions(-)

2010-08-06  gb10  <gb10>
 Added a iist of supported GFF types
 blixem_.h        |   9 ++-
 blxGff3Parser.c  | 225 +++++++++++++++++++++++++++++--------------------------
 blxGff3Parser_.h |  21 ++++--
 blxmain.c        |  10 ++-
 blxparser.c      |  18 ++---
 blxselect.c      |   7 +-
 blxview.c        |  10 ++-
 blxview.h        |   3 +-
 blxwindow.c      |  15 +++-
 blxwindow.h      |   2 +
 dotterMain.c     |   7 +-
 11 files changed, 187 insertions(+), 140 deletions(-)

2010-08-06  gb10  <gb10>
 Fixed a bug with parsing EMBL tags that span multiple lines
 blxFetch.c | 76 +++++++++++++++++++++++++++++++++-----------------------------
 1 file changed, 41 insertions(+), 35 deletions(-)

2010-08-05  gb10  <gb10>
 Fixed a bug where the default response was being lost on the second call for some dialogs
 blxwindow.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

2010-08-05  gb10  <gb10>
 Removed a spurious popup message that happens when pfetching full entries on startup fails (because pfetching just the fasta sequence may still work fine)
 blxFetch.c | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

2010-08-05  gb10  <gb10>
 Fixed a bug with the clipped-match marker where it was drawn the wrong side of the base when the display is reversed
 sequencecellrenderer.c | 30 ++++++++++++++++++++++++++----
 1 file changed, 26 insertions(+), 4 deletions(-)

2010-08-05  gb10  <gb10>
 Added pfetch of additional EMBL info for pfetch-http mode. Added marker to indicate if a match has a missing section where it has been clipped to the reference sequence range. Created a replacement for the old acedb message system. Made relevant dialogs persistent and added functionality to make them refresh their data when necessary.
 blixem_.h              |  14 +-
 blxFetch.c             | 732 ++++++++++++++++++++++---------------------------
 blxdotter.c            | 103 +++++--
 blxdotter.h            |   2 +-
 blxmain.c              |  47 +---
 blxview.c              | 156 +++++++++--
 blxview.h              |  23 +-
 blxwindow.c            | 498 ++++++++++++++++++++++++---------
 blxwindow.h            |  45 ++-
 detailview.c           |  23 +-
 detailviewtree.c       |   5 +-
 sequencecellrenderer.c |  32 +++
 utilities.c            | 405 +++++++++++++++++++++++++--
 utilities.h            |   8 +-
 14 files changed, 1416 insertions(+), 677 deletions(-)

2010-07-27  gb10  <gb10>
 fixed some uninitialised value warnings
 sequencecellrenderer.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

2010-07-26  gb10  <gb10>
 Added missing function definition for showInfoDialog
 blxwindow.h | 1 +
 1 file changed, 1 insertion(+)

2010-07-26  gb10  <gb10>
 Added sequence-info dialog
 blxwindow.c  | 53 ++++++++++++++++++++++++++++++++++++++-
 detailview.c | 28 ++++++---------------
 utilities.c  | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 utilities.h  |  2 ++
 4 files changed, 144 insertions(+), 21 deletions(-)

2010-07-26  gb10  <gb10>
 Fixed a bug where the detail-view-trees were scrolling vertically on a middle- or right- click
 detailviewtree.c | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

2010-07-23  gb10  <gb10>
 Removed more of the acedb package from blixem. Fixed a bug in the new pfetch code where it was getting data in the wrong order when data was loaded from the settings dialog rather than at startup.
 bigpicture.c           |   2 +-
 blixem_.h              |  26 ++++--
 blxFetch.c             | 192 ++++++++++++++++++++++++++++-----------
 blxGff3Parser.c        |   7 +-
 blxdotter.c            |   4 +-
 blxmain.c              |  38 ++++----
 blxparser.c            | 179 +++++++++++++++++++++---------------
 blxselect.c            | 191 ++++++++++++++++++++++++++++-----------
 blxview.c              | 180 +++++++++++++++++++-----------------
 blxview.h              |  10 +-
 blxwindow.c            |  37 +++++---
 detailview.c           |   3 +
 detailviewtree.c       |   5 +
 dotter.c               | 241 +++++++++++++++++++++++++++++++------------------
 exonview.c             |   1 +
 sequencecellrenderer.c |   4 +-
 utilities.c            | 142 ++++++++++++++++++++++++-----
 utilities.h            |   2 +
 18 files changed, 832 insertions(+), 432 deletions(-)

2010-07-21  gb10  <gb10>
 Renamed ColumnId to BlxColumnId
 blixem_.h        |  8 ++++----
 blxwindow.h      |  2 +-
 detailview.c     | 24 ++++++++++++------------
 detailview.h     | 12 ++++++------
 detailviewtree.c | 10 +++++-----
 5 files changed, 28 insertions(+), 28 deletions(-)

2010-07-21  gb10  <gb10>
 Removed an unused variable
 blxFetch.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2010-07-21  gb10  <gb10>
 Added help for the fetch-additional-data option.
 blxwindow.c | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

2010-07-21  gb10  <gb10>
 Added a warning if pfetch net id and port are not provided in the command line, env vars or config file.
 blxFetch.c | 32 ++++++++++++++++++++++++++++----
 1 file changed, 28 insertions(+), 4 deletions(-)

2010-07-21  gb10  <gb10>
 Fixed an issue where pfetch port and net_id were not being set if user changes to the pfetch mode from a different default mode.
 blixem_.h  |  3 ++-
 blxFetch.c | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 blxview.c  | 62 +---------------------------------------------------
 3 files changed, 76 insertions(+), 63 deletions(-)

2010-07-21  gb10  <gb10>
 Added functionality to parse additional info from the EMBL files such as organism and tissue-type. Added a command-line option to fetch this on startup and an option in the settings dialog to populate the data later, since it may be slower fetching the full EMBL files. (Although for nucleotide sequences it does not seem to be slower so in that case it always fetches the extra info.). Also fixed a bug where a crash was possible if the input s coords were out of the range of the given s sequence.
 blixem_.h              |  32 +-
 blxFetch.c             | 979 +++++++++++++++++++++++++++++++++++++++++--------
 blxdotter.c            |  10 +-
 blxmain.c              |  20 +-
 blxview.c              | 312 +++++++++++-----
 blxview.h              |  12 +-
 blxwindow.c            | 138 ++++++-
 blxwindow.h            |   7 +-
 detailview.c           | 115 +++++-
 detailview.h           |   7 +-
 detailviewtree.c       | 205 ++++++++---
 sequencecellrenderer.c |  58 ++-
 utilities.c            |  62 +++-
 utilities.h            |  20 +-
 14 files changed, 1615 insertions(+), 362 deletions(-)

2010-07-15  gb10  <gb10>
 Fixed a bug where middle-clicking in the tree headers was sometimes not working. Improved middle-clicking so that it now works on empty trees as well.
 detailview.c     | 190 ++++++++++++++++++++++++++++++++---
 detailview.h     |   1 +
 detailviewtree.c | 296 +++++++++++++------------------------------------------
 3 files changed, 249 insertions(+), 238 deletions(-)

2010-07-15  gb10  <gb10>
 Added basic type for polyA tails
 blxGff3Parser.c        |  9 ++++++++
 blxview.c              |  6 ++---
 blxview.h              |  4 +++-
 blxwindow.c            |  5 +++++
 detailview.c           |  4 ++--
 detailviewtree.c       | 61 ++++++++++++++++++++++++++++++++++----------------
 sequencecellrenderer.c | 16 ++++++++++++-
 utilities.c            | 14 ++++++++----
 utilities.h            |  1 +
 9 files changed, 90 insertions(+), 30 deletions(-)

2010-07-14  gb10  <gb10>
 Added option to select fetch mode. Fixed an issue where the background color changed slightly if you hit ok on the settings dialog.
 blixem_.h    |  3 ++-
 blxFetch.c   | 82 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 blxwindow.c  | 47 ++++++++++++++++++----------------
 detailview.c |  6 -----
 4 files changed, 108 insertions(+), 30 deletions(-)

2010-07-13  gb10  <gb10>
 RT58135: When pfetching a protein variant, pfetch with the -F option fails, so re-try without the -F option so that at least we get the fasta sequence. Also fixed a bug where the show-unaligned-sequence option was not working when Blixem was run in pfetch-http mode
 blixem_.h   |  12 +++++-
 blxFetch.c  | 126 +++++++++++++++++++++++++++++++++++++++++++++++-------------
 blxview.c   |  19 ++++-----
 blxwindow.c |   9 -----
 4 files changed, 120 insertions(+), 46 deletions(-)

2010-07-12  gb10  <gb10>
 Removed use of the Gex package from blxFetch.c
 blixem_.h   |  3 +-
 blxFetch.c  | 98 ++++++++++++++++++++++++++++++++++---------------------------
 blxwindow.c |  2 +-
 utilities.c | 65 +++++++++++++++++++++++++---------------
 utilities.h |  8 +++--
 5 files changed, 104 insertions(+), 72 deletions(-)

2010-07-12  gb10  <gb10>
 Fixed a bug where pfetch was sometimes failing to display the results because it was trying to apply pango markup
 blxFetch.c  | 78 +++++++++++++++++++++++++++++++------------------------------
 blxwindow.c |  2 +-
 utilities.c | 15 ++++++++----
 utilities.h |  2 ++
 4 files changed, 54 insertions(+), 43 deletions(-)

2010-07-12  gb10  <gb10>
 added comments
 blixem_.h | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

2010-07-12  gb10  <gb10>
 Made creation of tree columns more generic. Added Group and Source columns.
 bigpicture.c           |  16 ++--
 bigpicturegrid.c       |  10 +--
 blixem_.h              |  44 +++++++---
 blxview.c              |  28 +++----
 blxview.h              |  60 ++++++-------
 blxwindow.c            |  84 +++++++++----------
 blxwindow.h            |   2 +-
 detailview.c           | 224 ++++++++++++++++++-------------------------------
 detailview.h           |  35 ++------
 detailviewtree.c       | 190 +++++++++++++++++++++--------------------
 detailviewtree.h       |   8 +-
 exonview.c             |   2 +-
 sequencecellrenderer.c |  34 ++++----
 utilities.c            |  12 +--
 utilities.h            |   2 +-
 15 files changed, 346 insertions(+), 405 deletions(-)

2010-07-09  gb10  <gb10>
 Added 'source' column
 blxGff3Parser.c  |  3 +-
 blxview.c        | 37 ++-----------------------
 blxview.h        |  7 +++--
 detailview.c     | 60 ++++++++++++++++++++++++++--------------
 detailview.h     | 48 +++++++++++++++-----------------
 detailviewtree.c | 83 ++++++++++++++++++++++++++++++--------------------------
 6 files changed, 114 insertions(+), 124 deletions(-)

2010-07-09  gb10  <gb10>
 Rearranged tree column code to more easily allow additional columns to be added
 detailviewtree.c | 155 ++++++++++++++++++++++++++++++++-----------------------
 1 file changed, 91 insertions(+), 64 deletions(-)

2010-07-08  gb10  <gb10>
 Replaced custom cell-renderer properties with a generic text property
 blxwindow.c            |   2 +-
 detailview.c           |  30 ++++-----
 detailview.h           |  31 ++++-----
 detailviewtree.c       | 172 ++++++++++++++++++++++++-------------------------
 sequencecellrenderer.c | 123 +++++------------------------------
 sequencecellrenderer.h |  15 +++--
 6 files changed, 138 insertions(+), 235 deletions(-)

2010-07-08  gb10  <gb10>
 Rearranged detail-view column code
 detailview.c | 95 ++++++++++++++++++++++++++++++++++++++++--------------------
 1 file changed, 63 insertions(+), 32 deletions(-)

2010-07-08  gb10  <gb10>
 Added more help text
 blxwindow.c | 1 +
 1 file changed, 1 insertion(+)

2010-07-08  gb10  <gb10>
 Fixed a memory bug caused by the opts string not having a terminating null character.
 blxmain.c    | 29 +++++++++++++++++++++++++++--
 blxparser.c  | 14 +++++++++-----
 blxview.c    |  8 ++++----
 blxwindow.c  |  2 +-
 blxwindow.h  |  4 ++--
 detailview.c |  2 +-
 6 files changed, 44 insertions(+), 15 deletions(-)

2010-07-08  gb10  <gb10>
 Added splice-site highlighting. Fixed a bug where the bottom cell of the grid was not visible.
 bigpicturegrid.c       |   2 +-
 blxview.c              |  16 +-
 blxview.h              |   4 +-
 blxwindow.c            | 559 ++++++++++++++++++++++++++++++----------------
 blxwindow.h            |  24 +-
 detailview.c           | 586 ++++++++++++++++++++++++++++++++++++++-----------
 detailview.h           |  59 +++--
 detailviewtree.c       |  31 +--
 sequencecellrenderer.c |   6 +-
 9 files changed, 923 insertions(+), 364 deletions(-)

2010-07-01  gb10  <gb10>
 Made the highlight box extend over the exon view (previously it was just shown on the grids, which is not adequate now that the exon view can be bumped and can take up quite a large area). To facilitate this and make it less cluttered I changed the highlight box from a blue outline (shown separately on each grid) to a shaded region that spans across all of the visible big picture widgets.
 bigpicture.c     | 104 ++++++++++++++++++++++++++++++++-
 bigpicture.h     |  10 +++-
 bigpicturegrid.c | 175 +++++++------------------------------------------------
 bigpicturegrid.h |   5 --
 blxGff3Parser.c  |  12 +++-
 blxselect.c      |   4 +-
 blxwindow.c      |  16 +++--
 exonview.c       | 125 ++++++++++++++++++++++++---------------
 exonview.h       |   5 ++
 utilities.c      |  20 +++++++
 utilities.h      |   1 +
 11 files changed, 263 insertions(+), 214 deletions(-)

2010-07-01  gb10  <gb10>
 Added code to get MSP colors from key file
 bigpicture.c           |   4 +-
 bigpicturegrid.c       |  10 +-
 blixem_.h              |   9 +-
 blxmain.c              |  55 ++++++++---
 blxview.c              | 140 +++++++++++++++++++++++----
 blxview.h              |  59 +++++++++++-
 blxwindow.c            |  82 +++++++---------
 blxwindow.h            |   4 +-
 detailview.c           |  16 ++--
 detailviewtree.c       |   2 +-
 exonview.c             |  43 ++-------
 sequencecellrenderer.c |  32 +++----
 utilities.c            | 250 +++++++++++++++++++++++++++++++++++--------------
 utilities.h            |  58 +-----------
 14 files changed, 478 insertions(+), 286 deletions(-)

2010-06-29  gb10  <gb10>
 Fixed a bug in searching for sequence names
 blxwindow.c | 51 +++++++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 43 insertions(+), 8 deletions(-)

2010-06-29  gb10  <gb10>
 Fixed bug where sequence name prefix was not being shown in feedback box
 utilities.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2010-06-29  gb10  <gb10>
 Fixed bug with new key file option not being read from command line
 blxmain.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2010-06-28  gb10  <gb10>
 Added colors/styles key file parser
 blixem_.h        | 12 +++++--
 blxFetch.c       |  4 ++-
 blxGff3Parser.c  | 78 ++++-----------------------------------------
 blxGff3Parser_.h |  3 +-
 blxmain.c        | 84 +++++++++++++++++++++++++++++++++++++++++++++----
 blxparser.c      | 12 +++----
 blxview.c        | 96 ++++++++++++++++++++++++++++++++++++++++++++------------
 blxview.h        | 17 +++++++---
 blxwindow.c      | 30 +++++++++++-------
 dotterMain.c     |  4 +--
 utilities.c      | 65 +++++++++++++++++++++-----------------
 utilities.h      |  4 +--
 12 files changed, 251 insertions(+), 158 deletions(-)

2010-06-25  gb10  <gb10>
 Added Help documentation for new features. Added code to allow GtkTextView to use pango markup
 blxwindow.c | 319 ++++++++++++++++++++++++++++++++----------------------------
 utilities.c | 271 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 utilities.h |  19 ++++
 3 files changed, 457 insertions(+), 152 deletions(-)

2010-06-24  gb10  <gb10>
 Added DNA search facility and tweaked some colours.
 blxdotter.c |  14 +-
 blxwindow.c | 604 +++++++++++++++++++++++++++++++++++++++++++++++++-----------
 utilities.c | 145 ++++++++-------
 utilities.h |  33 ++--
 4 files changed, 607 insertions(+), 189 deletions(-)

2010-06-21  gb10  <gb10>
 Moved addBlxSequenceData and mspHasFs to blxview.c so they can be found by the xace build
 blxparser.c | 76 +------------------------------------------------------------
 blxview.c   | 62 ++++++++++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 62 insertions(+), 76 deletions(-)

2010-06-21  gb10  <gb10>
 Added option to view unaligned parts of match sequences
 bigpicturegrid.c       |   8 +-
 blxGff3Parser.c        |  45 +++++------
 blxdotter.c            |  10 ++-
 blxparser.c            |  34 ++++++---
 blxview.c              |  22 ++----
 blxview.h              |  20 +++--
 blxwindow.c            | 131 +++++++++++++++++++++++++++-----
 blxwindow.h            |   1 +
 detailview.c           |  78 +++++++++++++++++--
 detailview.h           |  11 +++
 detailviewtree.c       | 136 ++++++++++++++++++++++++++-------
 dotter.c               |  63 ++++++++--------
 dotterMain.c           |  10 ++-
 exonview.c             |   8 +-
 sequencecellrenderer.c |  97 +++++++++++++++++++-----
 utilities.c            | 201 +++++++++++++++++++++++++++++++++++++------------
 utilities.h            |  31 +++++---
 17 files changed, 669 insertions(+), 237 deletions(-)

2010-06-16  gb10  <gb10>
 Fixed bug in color parser code
 blxview.c | 63 ++++++++++++++++++++++++++++++++++++++++++++-------------------
 1 file changed, 44 insertions(+), 19 deletions(-)

2010-06-16  gb10  <gb10>
 Added basic facility to parse colors in GFF files
 blxGff3Parser.c | 71 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 blxview.c       | 12 +++++++++-
 blxview.h       |  6 ++++-
 3 files changed, 86 insertions(+), 3 deletions(-)

2010-06-15  gb10  <gb10>
 Fixed an incorrect SO value in the GFF parser. Misc tidying.
 blxGff3Parser.c |  2 +-
 blxwindow.c     | 18 +++++++++---------
 utilities.c     | 13 ++++++++++---
 utilities.h     |  4 ++--
 4 files changed, 22 insertions(+), 15 deletions(-)

2010-06-15  gb10  <gb10>
 Added match set type
 blxGff3Parser.c | 72 ++++++++++++++++++++++++++++++++++++++++++++++++++++-----
 blxview.h       |  5 ++--
 2 files changed, 69 insertions(+), 8 deletions(-)

2010-06-14  gb10  <gb10>
 GFF 3 parser now handles SO numbers and frameshift operators
 blxGff3Parser.c | 55 +++++++++++++++++++++++++++++--------------------------
 utilities.c     |  7 ++++++-
 2 files changed, 35 insertions(+), 27 deletions(-)

2010-06-14  gb10  <gb10>
 Fixed some bugs with the GFF3 parser. Added the 'R|r' option back in (to show/hide the reverse strand grid)
 bigpicture.c           |   1 -
 blixem_.h              |  20 +++++-
 blxFetch.c             |  12 ++--
 blxGff3Parser.c        | 191 +++++++++++++++++++++++++++++++------------------
 blxGff3Parser_.h       |   9 ---
 blxdotter.c            |   3 +-
 blxmain.c              |  23 ++----
 blxparser.c            |  59 ++++-----------
 blxview.c              |  14 ++--
 blxwindow.c            |  15 ++--
 blxwindow.h            |   2 +-
 detailview.c           |   3 +-
 detailviewtree.c       |   3 +-
 sequencecellrenderer.c |   3 +-
 utilities.c            |  25 +++++++
 utilities.h            |   1 +
 16 files changed, 209 insertions(+), 175 deletions(-)

2010-06-11  gb10  <gb10>
 Added GFF3 parser
 blxGff3Parser_.h | 79 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)

2010-06-11  gb10  <gb10>
 Added GFF3 parser
 blxGff3Parser.c | 653 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 653 insertions(+)

2010-06-11  gb10  <gb10>
 Added GFF3 parser. Removed g_prefix_error and g_propagate_prefixed_error because they're not in our current linux GTK version
 bigpicture.c           |    8 +-
 bigpicturegrid.c       |    4 +-
 blixem_.h              |  325 ++++++++------
 blxFetch.c             |  451 +++++++++----------
 blxdotter.c            |   51 +--
 blxmain.c              |   58 ++-
 blxparser.c            | 1143 ++++++++++++++++++++++++++++--------------------
 blxselect.c            |    9 +-
 blxview.c              |  409 ++++++++++++-----
 blxview.h              |  131 +++---
 blxwindow.c            |  486 ++++++++++----------
 blxwindow.h            |   18 +-
 detailview.c           |   47 +-
 detailviewtree.c       |   60 +--
 dotter.c               |   37 +-
 dotterMain.c           |   10 +-
 exonview.c             |   59 ++-
 sequencecellrenderer.c |   49 ++-
 translate.c            |  144 +-----
 utilities.c            |  508 ++++++++++++++-------
 utilities.h            |   75 +++-
 21 files changed, 2342 insertions(+), 1740 deletions(-)

2010-05-26  gb10  <gb10>
 More refactoring of parser code. Fixed a bug where an invalid match frame was being set when reading old format exblx files
 bigpicturegrid.c       |   2 +-
 blixem_.h              |   6 +-
 blxdotter.c            |   6 +-
 blxparser.c            | 460 ++++++++++++++++++++++++++++---------------------
 blxview.h              |  12 +-
 blxwindow.c            |  32 ++--
 blxwindow.h            |  17 +-
 detailview.c           |   6 +-
 detailviewtree.c       |  30 ++--
 exonview.c             |   4 +-
 sequencecellrenderer.c |   2 +-
 utilities.c            |  46 ++---
 utilities.h            |  10 +-
 13 files changed, 349 insertions(+), 284 deletions(-)

2010-05-25  gb10  <gb10>
 More refactoring of parser code
 blxparser.c | 99 ++++++++++++++++++++++++++++++-------------------------------
 1 file changed, 48 insertions(+), 51 deletions(-)

2010-05-25  gb10  <gb10>
 Added a proper MSP type. Separated this out from the data type used by the parser, which is only used to record what kind of data is currently being parsed.
 blixem_.h    |   5 +-
 blxparser.c  | 273 +++++++++++++++++++++++++++++++++++++++--------------------
 blxview.c    |   5 +-
 blxview.h    |  94 ++++++++++----------
 dotter.c     |  28 +++---
 dotterMain.c |   9 +-
 6 files changed, 252 insertions(+), 162 deletions(-)

2010-05-25  gb10  <gb10>
 Tidied Feature Series code
 blixem_.h    |  49 ++-----------------
 blxparser.c  | 112 +++++++++++++++++++++++++++----------------
 blxview.c    |  34 +------------
 blxview.h    |  27 +++++++----
 dotter.c     | 153 +++++++++++++++++++++++++++++++++++------------------------
 dotterMain.c |   6 +--
 utilities.h  |   6 ++-
 7 files changed, 192 insertions(+), 195 deletions(-)

2010-05-25  gb10  <gb10>
 Started tidying dotter code
 dotterMain.c | 514 ++++++++++++++++++++++++++++++++++-------------------------
 1 file changed, 296 insertions(+), 218 deletions(-)

2010-05-24  gb10  <gb10>
 Tidied help text code
 blxwindow.c | 349 ++++++++++++++++++++++++++++++------------------------------
 1 file changed, 175 insertions(+), 174 deletions(-)

2010-05-21  gb10  <gb10>
 Fixed a bug in the refactored parser code
 blxparser.c | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

2010-05-21  gb10  <gb10>
 Added dotter vs self and hsps-only options
 blxdotter.c | 295 ++++++++++++++++++++++++++++++++++++++++++------------------
 1 file changed, 206 insertions(+), 89 deletions(-)

2010-05-20  gb10  <gb10>
 More tidying of the parser code
 blxparser.c | 1080 +++++++++++++++++++++++++++++++----------------------------
 blxview.h   |   10 +-
 2 files changed, 568 insertions(+), 522 deletions(-)

2010-05-20  gb10  <gb10>
 Improved error handling. Started replacing acedb messages with GLib messages
 bigpicturegrid.c       |   2 +-
 blxFetch.c             |  40 +++---
 blxdotter.c            | 326 ++++++++++++++++++++++++++++---------------------
 blxdotter.h            |   2 +-
 blxmain.c              |  24 ++--
 blxparser.c            |  56 ++++-----
 blxselect.c            |   4 +-
 blxview.c              |  21 +++-
 blxwindow.c            |  53 ++++++--
 blxwindow.h            |   3 +-
 detailview.c           | 136 +++++++++++----------
 detailviewtree.c       | 101 ++++++++-------
 sequencecellrenderer.c |  76 ++++++------
 utilities.c            |  44 ++++++-
 utilities.h            |   2 +
 15 files changed, 525 insertions(+), 365 deletions(-)

2010-05-19  gb10  <gb10>
 Removed some unused code
 blxmain.c | 16 +---------------
 1 file changed, 1 insertion(+), 15 deletions(-)

2010-05-19  gb10  <gb10>
 Related to RT ticket 169930: blixem was passing an incorrect offset to dotter
 blxdotter.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-05-19  gb10  <gb10>
 Code tidying: renamed Strand to BlxStrand and SortByType to BlxSortMode; rearranged parser code
 bigpicture.c           |   8 +-
 bigpicturegrid.c       |   6 +-
 bigpicturegrid.h       |   6 +-
 blixem_.h              |   8 +-
 blxdotter.c            |   8 +-
 blxdotter.h            |   2 +-
 blxparser.c            | 729 ++++++++++++++++++++++++++-----------------------
 blxview.c              |  16 +-
 blxwindow.c            |  34 +--
 blxwindow.h            |  26 +-
 detailview.c           | 104 +++----
 detailview.h           |  16 +-
 detailviewtree.c       |  22 +-
 detailviewtree.h       |   4 +-
 dotter.c               |  50 ++--
 dotter_.h              |   4 +-
 exonview.c             |   9 +-
 exonview.h             |   4 +-
 iupac.h                |   4 +-
 sequencecellrenderer.c |   2 +-
 translate.c            |   8 +-
 utilities.c            |  17 +-
 utilities.h            |   8 +-
 23 files changed, 570 insertions(+), 525 deletions(-)

2010-05-18  gb10  <gb10>
 Removed call to gdk_color_to_string, which is incompatible with our current version of GDK
 blxwindow.c | 30 +++++++++++++++++++++++++-----
 1 file changed, 25 insertions(+), 5 deletions(-)

2010-05-18  gb10  <gb10>
 Code tidying
 blxparser.c |  18 ++----
 blxview.c   | 181 +-----------------------------------------------------------
 blxview.h   |  21 +------
 3 files changed, 7 insertions(+), 213 deletions(-)

2010-05-18  gb10  <gb10>
 Destroy colors properly
 blxwindow.c | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

2010-05-18  gb10  <gb10>
 Fix for RT169901: make exons the same direction as their ref seq strand
 translate.c | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

2010-05-17  gb10  <gb10>
 Fixed a few bugs with selections
 blxwindow.c      |  14 ++++++++
 blxwindow.h      |   1 +
 detailviewtree.c | 108 ++++++++++++++++++++++++++++++++++++++++++++++---------
 3 files changed, 107 insertions(+), 16 deletions(-)

2010-05-17  gb10  <gb10>
 Made coord conversion functions more robust against invalid input
 utilities.c | 88 +++++++++++++++++++++++++++++++++----------------------------
 1 file changed, 47 insertions(+), 41 deletions(-)

2010-05-17  gb10  <gb10>
 Changed the way selections work because this was causing a bug where sometimes the cell renderer would not render a row that should have been visible
 bigpicturegrid.c | 102 ++++++----------
 blxview.c        |   4 +-
 blxwindow.c      |  78 +++++++-----
 blxwindow.h      |   9 +-
 detailview.c     |  29 ++++-
 detailview.h     |   6 +
 detailviewtree.c | 352 ++++++++++++++++++++++++++-----------------------------
 detailviewtree.h |   5 +-
 8 files changed, 296 insertions(+), 289 deletions(-)

2010-05-14  gb10  <gb10>
 Made SNP stuff more flexible so they can be drawn with different colour outline and fill colours
 blxwindow.c      |   1 -
 detailview.c     | 207 ++++++++++++++++++++++++++++++++++++++++++++-----------
 detailview.h     |  18 +++++
 detailviewtree.c |  98 ++------------------------
 detailviewtree.h |  13 ----
 5 files changed, 190 insertions(+), 147 deletions(-)

2010-05-13  gb10  <gb10>
 Added black-and-white colour option for printing. Added facility to color exons according to whether they are CDS or UTR (and made all exons CDS for now until we pass this info in). Added colors to settings dialog. Made STOPs red and METs green in the three-frame translation for protein matches.
 bigpicture.c           |  28 ++--
 bigpicture.h           |   8 -
 bigpicturegrid.c       | 103 ++++++------
 blixem_.h              |   4 +-
 blxFetch.c             |   4 +-
 blxparser.c            |   8 +-
 blxview.c              |   6 +-
 blxwindow.c            | 424 +++++++++++++++++++++++++++++++++++++++++++++----
 blxwindow.h            |   4 +
 detailview.c           |  49 ++----
 detailview.h           |  31 +---
 detailviewtree.c       |  81 +++++-----
 detailviewtree.h       |   2 +-
 exonview.c             |  77 ++++-----
 sequencecellrenderer.c | 199 +++++++++++------------
 utilities.c            | 168 ++++++++++++++++----
 utilities.h            | 128 +++++++++++----
 17 files changed, 884 insertions(+), 440 deletions(-)

2010-05-11  gb10  <gb10>
 Colour METs green and STOPs red
 blixem_.h        |  5 ++--
 detailview.c     | 22 +++++++++++++----
 detailview.h     |  9 ++++---
 detailviewtree.c | 72 +++++++++++++++++++++++++++++++-------------------------
 detailviewtree.h | 15 +++++++++---
 utilities.h      |  9 +++++++
 6 files changed, 87 insertions(+), 45 deletions(-)

2010-05-10  gb10  <gb10>
 Added bump options to view dialog box
 blixem_.h   | 4 ++--
 blxwindow.c | 7 ++-----
 exonview.c  | 6 ++++++
 exonview.h  | 3 +++
 4 files changed, 13 insertions(+), 7 deletions(-)

2010-05-10  gb10  <gb10>
 Added bump options to view dialog box
 blxwindow.c | 117 ++++++++++++++++++++++++++++++++++++++++++++----------------
 1 file changed, 87 insertions(+), 30 deletions(-)

2010-05-10  gb10  <gb10>
 Added ability to bump exon view
 bigpicture.c     |  37 ++++++--
 bigpicture.h     |   3 +
 bigpicturegrid.c |  24 ++---
 blxwindow.c      |  29 ++++--
 detailview.c     |   1 +
 exonview.c       | 281 ++++++++++++++++++++++++++++++++++++++++---------------
 exonview.h       |   5 +-
 7 files changed, 272 insertions(+), 108 deletions(-)

2010-05-10  gb10  <gb10>
 Added additional info to SequenceStruct
 blxdotter.c      |   4 +-
 blxview.h        |  11 +++--
 blxwindow.c      |  20 +++++----
 detailview.c     |  11 +++--
 detailviewtree.c |   5 ++-
 exonview.c       |   1 -
 utilities.c      | 128 +++++++++++++++++++++++++++++++++++++++++++------------
 utilities.h      |  12 +++++-
 8 files changed, 141 insertions(+), 51 deletions(-)

2010-05-10  gb10  <gb10>
 Automatically calculate the lowest ID of all matches and cut off the grid range at that value (to the nearest grid cell) to save space in the big picture. Also refactored the code so that sequences can be passed as objects rather than just referred to by name
 bigpicture.c           |  93 +++++++-
 bigpicture.h           |  17 +-
 bigpicturegrid.c       |  98 +++------
 bigpicturegrid.h       |   3 -
 blixem_.h              |  14 +-
 blxdotter.c            |  29 ++-
 blxparser.c            |   6 +-
 blxview.c              |   4 +-
 blxview.h              |  21 +-
 blxwindow.c            | 573 ++++++++++++++++++++++++++++++++++++++-----------
 blxwindow.h            |  18 +-
 detailview.c           | 332 ++++------------------------
 detailview.h           |  11 +-
 detailviewtree.c       |  67 +++---
 detailviewtree.h       |   3 -
 exonview.c             |  24 +--
 sequencecellrenderer.c |  31 +--
 utilities.c            |  61 ++++--
 utilities.h            |   3 +-
 19 files changed, 767 insertions(+), 641 deletions(-)

2010-05-06  gb10  <gb10>
 Added About dialog
 blixem_.h    |  27 ++++++++++---
 blxmain.c    |   5 +--
 blxwindow.c  | 127 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++---
 blxwindow.h  |   3 +-
 detailview.c |   8 ++--
 utilities.c  |  76 +++++++++++++++++++----------------
 utilities.h  |   5 +++
 7 files changed, 198 insertions(+), 53 deletions(-)

2010-05-06  gb10  <gb10>
 Fixed a bug where running dotter on protein matches was sometimes getting the wrong q strand
 blxdotter.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2010-05-05  gb10  <gb10>
 Moved some generic utility functions to utilities.c
 blxwindow.c | 53 -----------------------------------------------------
 utilities.c | 52 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 utilities.h |  3 +++
 3 files changed, 55 insertions(+), 53 deletions(-)

2010-05-05  gb10  <gb10>
 Added option to use big picture display range for dotter
 blxdotter.c | 45 ++++++++++++++++++++++++++++++++++++---------
 1 file changed, 36 insertions(+), 9 deletions(-)

2010-05-05  gb10  <gb10>
 Refactored dotter dialog code to make it easier to add new widgets
 blxdotter.c | 350 +++++++++++++++++++++++++++++++-----------------------------
 1 file changed, 178 insertions(+), 172 deletions(-)

2010-05-05  gb10  <gb10>
 Made dotter dialog non-modal
 blxdotter.c | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

2010-05-04  gb10  <gb10>
 Added a blxview context; code tidying; fixed a bug with SNPs not showing when display reversed.
 bigpicture.c           |  46 +++---
 bigpicture.h           |   2 +-
 bigpicturegrid.c       |  44 +++---
 blxdotter.c            | 145 +++++++++----------
 blxwindow.c            |  56 ++++----
 blxwindow.h            |  12 +-
 detailview.c           | 382 +++++++++++++++----------------------------------
 detailview.h           |  21 +--
 detailviewtree.c       | 234 ++++++++----------------------
 detailviewtree.h       |  29 +---
 exonview.c             |  36 ++---
 sequencecellrenderer.c |  36 ++---
 utilities.c            |  20 +--
 utilities.h            |  10 +-
 14 files changed, 369 insertions(+), 704 deletions(-)

2010-04-30  gb10  <gb10>
 Renamed MainWindow to BlxWindow, and created blixem context
 bigpicture.c           |  52 ++++----
 bigpicture.h           |   8 +-
 bigpicturegrid.c       |  64 ++++-----
 blixem_.h              |  30 +----
 blxFetch.c             |  20 +--
 blxdotter.c            |  96 +++++++-------
 blxview.c              |  22 ++--
 blxwindow.c            | 343 ++++++++++++++++++++++++++++---------------------
 blxwindow.h            |  74 +++++------
 detailview.c           | 219 ++++++++++++++++---------------
 detailview.h           |  14 +-
 detailviewtree.c       | 110 ++++++++--------
 detailviewtree.h       |   4 +-
 exonview.c             |  32 ++---
 sequencecellrenderer.c |  34 ++---
 15 files changed, 572 insertions(+), 550 deletions(-)

2010-04-30  gb10  <gb10>
 Renamed MainWindow to the more informative BlxWindow
 blxviewMainWindow.c => blxwindow.c | 624 ++++++++++++++++++-------------------
 blxviewMainWindow.h => blxwindow.h | 102 +++---
 2 files changed, 363 insertions(+), 363 deletions(-)

2010-04-30  gb10  <gb10>
 Allow user to select a SNP by clicking the DNA coord. Show/hide SNP track by double-clicking DNA header
 detailview.c     | 215 +++++++++++++++++++++++++++++++++++++++++--------------
 detailview.h     |  18 ++++-
 detailviewtree.c | 109 ++++++++++++++++------------
 detailviewtree.h |   6 +-
 4 files changed, 245 insertions(+), 103 deletions(-)

2010-04-29  gb10  <gb10>
 Added option in Settings dialog to show/hide SNP track
 blxviewMainWindow.c | 11 ++++++++
 detailview.c        | 76 +++++++++++++++++++++++++++++++++++++++--------------
 detailview.h        | 11 +++++---
 detailviewtree.c    | 14 +++++-----
 4 files changed, 83 insertions(+), 29 deletions(-)

2010-04-29  gb10  <gb10>
 Added SNP track. Also improved highlight colours
 blxdotter.c            |  25 +-
 blxviewMainWindow.c    |   6 +-
 blxviewMainWindow.h    |   2 +
 detailview.c           | 824 ++++++++++++++++++++++++++++++++++---------------
 detailview.h           |  14 +-
 detailviewtree.c       | 429 ++++++++++++++++---------
 detailviewtree.h       |   7 +-
 sequencecellrenderer.c |  20 +-
 utilities.c            | 171 +++++-----
 utilities.h            |   3 +-
 10 files changed, 1009 insertions(+), 492 deletions(-)

2010-04-28  gb10  <gb10>
 Added new version number and copyright info to usage info
 blixem_.h | 8 ++++----
 blxmain.c | 8 ++++++--
 2 files changed, 10 insertions(+), 6 deletions(-)

2010-04-26  gb10  <gb10>
 Don't add introns to alignment trees
 detailview.c | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

2010-04-26  gb10  <gb10>
 Fix related to RT166076: avoid a crash if an invalid frame number is given. Also still draw MSPs in the grid even if they are not in an alignment list, and colour exons/introns by group colour
 detailview.c           |  11 ++-
 detailviewtree.c       |  37 +++++-----
 exonview.c             | 188 ++++++++++++++++++++++---------------------------
 sequencecellrenderer.c |   2 +-
 utilities.c            |   8 ++-
 5 files changed, 121 insertions(+), 125 deletions(-)

2010-04-21  gb10  <gb10>
 Added a basic method for getting SNP data in to Blixem via the exblx_x or seqbl_x file formats
 bigpicturegrid.c |  2 +-
 blxdotter.c      | 10 ++++------
 blxparser.c      |  4 ++--
 detailview.c     | 20 ++++++++++++--------
 utilities.c      | 18 ++++++++++++------
 utilities.h      |  1 +
 6 files changed, 32 insertions(+), 23 deletions(-)

2010-04-21  gb10  <gb10>
 When jumping to the start/end of a match, make sure we jump to the exact DNA base (not the first/last base in the msp's reading frame, which may be different for exons)
 detailview.c | 178 +++++++++++++++++++++++++++++++++++++++--------------------
 1 file changed, 117 insertions(+), 61 deletions(-)

2010-04-21  gb10  <gb10>
 Made Blixem calculate the reading frame that it should belong to and check this agains the reading frame passed in the input file
 blxdotter.c      |   2 +-
 detailview.c     | 215 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 detailviewtree.c | 204 +---------------------------------------------------
 utilities.c      |  11 ++-
 utilities.h      |   3 +-
 5 files changed, 229 insertions(+), 206 deletions(-)

2010-04-20  gb10  <gb10>
 New blixem: fixed a bug where go-to-position was failing for protein matches with negative coords. Also removed some nasty offset code
 bigpicture.c           | 10 ++++----
 bigpicturegrid.c       | 15 +++++-------
 blxdotter.c            |  5 ++--
 blxviewMainWindow.c    | 64 +++++++++++++++++---------------------------------
 blxviewMainWindow.h    |  1 -
 detailview.c           | 19 +++++----------
 detailviewtree.c       | 11 ++++-----
 exonview.c             |  5 ++--
 sequencecellrenderer.c | 12 ++++------
 utilities.c            | 27 ++++++++++-----------
 utilities.h            | 10 +++-----
 11 files changed, 66 insertions(+), 113 deletions(-)

2010-04-14  gb10  <gb10>
 Improved char width calculations
 bigpicture.c | 2 +-
 blxFetch.c   | 4 ++--
 detailview.c | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

2010-04-14  gb10  <gb10>
 Added keyboard shortcut to scroll one page left/right
 blxviewMainWindow.c | 23 ++++++++++++-----------
 detailview.c        |  8 ++++----
 2 files changed, 16 insertions(+), 15 deletions(-)

2010-04-14  gb10  <gb10>
 Fixed a memory bug which was causing a crash on 64 bit linux
 detailview.c | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

2010-04-14  gb10  <gb10>
 New blixem: removed unnecessary stuff from public header. Put padseq back in use.
 bigpicturegrid.h    |  3 ++-
 blixem_.h           |  8 +++++++-
 blxdotter.c         | 13 ++++++-------
 blxview.h           | 18 +-----------------
 blxviewMainWindow.h |  2 +-
 detailview.h        |  2 +-
 detailviewtree.c    |  8 +++++---
 detailviewtree.h    |  2 +-
 exonview.h          |  2 +-
 utilities.h         |  8 ++++++++
 10 files changed, 33 insertions(+), 33 deletions(-)

2010-04-14  gb10  <gb10>
 RT165950: made big picture zoom buttons bigger
 bigpicture.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2010-04-14  gb10  <gb10>
 RT165945: do not change text colour when row selected; darken row colour instead.
 bigpicturegrid.c       | 47 ++++++++++++++++++++++++++++++-----------------
 detailviewtree.c       |  4 ++--
 sequencecellrenderer.c | 12 +++++++++++-
 utilities.c            | 38 ++++++++++++++++++++++++++++++++++++++
 utilities.h            |  2 ++
 5 files changed, 83 insertions(+), 20 deletions(-)

2010-04-13  gb10  <gb10>
 New blixem: make sure we don't find a non-monospace font in our preferred list of font families
 detailview.c | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

2010-04-13  gb10  <gb10>
 New blixem: fixed issues with protein alignments misaligning when first base is not base1. Fixed an issues with dotter not rev comping the s seq for some fetch methods
 bigpicture.c           | 10 +++++---
 bigpicturegrid.c       | 17 +++++++------
 blxdotter.c            | 68 +++++++++++++++++++++++++++++++-------------------
 blxviewMainWindow.c    | 22 ++++++++++------
 blxviewMainWindow.h    |  2 +-
 detailview.c           | 26 +++++++++++--------
 detailviewtree.c       |  5 ++--
 exonview.c             |  5 ++--
 sequencecellrenderer.c | 12 +++++----
 utilities.c            |  8 +++---
 utilities.h            |  4 ++-
 11 files changed, 112 insertions(+), 67 deletions(-)

2010-03-26  gb10  <gb10>
 New blixem: fixed bugs with protein matches not aligning if first coord is not base 1
 bigpicturegrid.c    |  8 ++++++--
 blxview.c           | 13 ++++++++-----
 blxviewMainWindow.c | 32 ++++++++++++++++++++++++++------
 blxviewMainWindow.h |  8 +++++---
 detailview.c        |  2 ++
 detailviewtree.c    | 22 ++++++++++++++--------
 utilities.c         | 12 ++++++++++--
 utilities.h         |  6 ++++--
 8 files changed, 75 insertions(+), 28 deletions(-)

2010-03-26  gb10  <gb10>
 New blixem: typo fix
 blxFetch.c | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

2010-03-26  gb10  <gb10>
 New blixem: bug fixes
 bigpicturegrid.c    | 25 ++++++++++++++++++-------
 blixem_.h           |  4 ++--
 blxFetch.c          |  5 ++---
 blxdotter.c         |  2 --
 blxviewMainWindow.c | 34 ++++++++++++++++++++++------------
 blxviewMainWindow.h |  2 +-
 detailviewtree.c    |  4 ++++
 utilities.c         |  4 ++--
 8 files changed, 51 insertions(+), 29 deletions(-)

2010-03-26  gb10  <gb10>
 New blixem: more dotter fixes
 blxdotter.c | 66 +++++++++++++++++++++++++++++++++++++++++++------------------
 utilities.c | 25 ++++++++++++++---------
 2 files changed, 63 insertions(+), 28 deletions(-)

2010-03-25  gb10  <gb10>
 New blixem: dotter bug fixes
 blxdotter.c         | 18 +++++++++++-------
 blxviewMainWindow.c |  2 +-
 2 files changed, 12 insertions(+), 8 deletions(-)

2010-03-25  gb10  <gb10>
 New blixem: made dotter call work for reverse s strands (as well as it worked before...)
 blxdotter.c         |  31 ++++++++++++---
 blxviewMainWindow.c |  16 +++++++-
 blxviewMainWindow.h |   2 +
 detailview.c        | 108 ++++++++++++++++++++++++++++++----------------------
 detailviewtree.c    |   3 --
 dotterMain.c        |   4 +-
 6 files changed, 105 insertions(+), 59 deletions(-)

2010-03-24  gb10  <gb10>
 New blixem: small bug fix with shortcuts
 blxviewMainWindow.c | 92 ++++++++++++++++++++++++++---------------------------
 1 file changed, 45 insertions(+), 47 deletions(-)

2010-03-24  gb10  <gb10>
 New blixem: toolbar and dialog improvements
 bigpicture.c        |   6 +-
 blxparser.c         |  15 +++-
 blxviewMainWindow.c | 230 ++++++++++++++++++++++++++++------------------------
 blxviewMainWindow.h |   3 +
 detailview.c        | 123 ++++++++++++++++++++--------
 5 files changed, 229 insertions(+), 148 deletions(-)

2010-03-24  gb10  <gb10>
 New blixem: added Home/End shortcut keys
 blxviewMainWindow.c | 36 ++++++++++++++++++++++++++++++++++++
 detailview.c        | 43 +++++++++++--------------------------------
 detailview.h        |  5 +++--
 3 files changed, 50 insertions(+), 34 deletions(-)

2010-03-24  gb10  <gb10>
 New blixem: better left/right scrolling
 blxview.c           |   4 +-
 blxviewMainWindow.c |  27 +++++--
 detailview.c        | 201 ++++++++++++++++++++++++++++++++++++++--------------
 detailview.h        |   7 +-
 detailviewtree.c    |   2 +-
 utilities.c         |   2 +-
 6 files changed, 180 insertions(+), 63 deletions(-)

2010-03-23  gb10  <gb10>
 New blixem: go to next/prev match now works on current selection
 blxviewMainWindow.c | 31 ++---------------------------
 detailview.c        | 56 +++++++++++++++++++++++++++++++++--------------------
 utilities.c         | 23 +++++++++++++++++++++-
 utilities.h         |  3 +++
 4 files changed, 62 insertions(+), 51 deletions(-)

2010-03-23  gb10  <gb10>
 New blixem: added find dialog
 blxviewMainWindow.c | 256 +++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 193 insertions(+), 63 deletions(-)

2010-03-23  gb10  <gb10>
 New blixem: got rid of hard-coded special sequence characters
 blixem_.h              |  8 +++++++-
 blxFetch.c             |  6 +++---
 blxdotter.c            |  2 +-
 blxparser.c            | 19 +++++++++++++------
 blxview.c              |  6 +++---
 sequencecellrenderer.c |  6 +++---
 6 files changed, 30 insertions(+), 17 deletions(-)

2010-03-23  gb10  <gb10>
 New blixem: replaced deprecated combo box used for sort list
 detailview.c | 145 ++++++++++++++++++++++++++++++++++-------------------------
 1 file changed, 83 insertions(+), 62 deletions(-)

2010-03-23  gb10  <gb10>
 New blixem: added proper destroy functions
 bigpicture.c        | 177 +++++++++--------
 bigpicture.h        |   1 +
 bigpicturegrid.c    |   1 +
 blixem_.h           |  28 +--
 blxFetch.c          |   6 +-
 blxdotter.c         |   5 +-
 blxdotter.h         |   1 +
 blxview.c           | 538 +++++++++++++---------------------------------------
 blxview.h           |   4 +-
 blxviewMainWindow.c | 104 ++++++----
 blxviewMainWindow.h |  30 ++-
 detailview.c        |  36 ++++
 detailviewtree.c    |  22 ++-
 detailviewtree.h    |   2 -
 14 files changed, 380 insertions(+), 575 deletions(-)

2010-03-22  gb10  <gb10>
 New blixem: added match sets. Tidied dialogs. Fixed some leaks
 blxviewMainWindow.c | 541 ++++++++++++++++++++++++++++++++++++----------------
 blxviewMainWindow.h |   6 +-
 detailview.c        |   2 +-
 utilities.c         |  49 +++--
 utilities.h         |   2 +
 5 files changed, 413 insertions(+), 187 deletions(-)

2010-03-19  gb10  <gb10>
 New blixem: added ability to create a group from zmap selections
 bigpicturegrid.c    |   2 +-
 blixem_.h           |   5 +-
 blxparser.c         |   3 +-
 blxview.c           | 234 +-------------------------------
 blxview.h           |   5 +-
 blxviewMainWindow.c | 287 ++++++++++++++++++++++++++-------------
 utilities.c         | 378 ++++++++++++++++++++++++++++++++++++----------------
 utilities.h         |  11 ++
 8 files changed, 477 insertions(+), 448 deletions(-)

2010-03-19  gb10  <gb10>
 New blixem: improved dialogs
 blxdotter.c         |   8 +-
 blxviewMainWindow.c | 403 ++++++++++++++++++++++++++++++++--------------------
 utilities.c         |  47 +++++-
 utilities.h         |   7 +-
 4 files changed, 299 insertions(+), 166 deletions(-)

2010-03-18  gb10  <gb10>
 New blixem: improvements to settings dialog
 blxviewMainWindow.c | 58 ++++++++++++++++++++++++++++++++++++++++++-----------
 utilities.c         | 58 ++++++++++++++++++++++++++++++++++++++++++++++++++---
 utilities.h         | 14 +++++++++++++
 3 files changed, 115 insertions(+), 15 deletions(-)

2010-03-18  gb10  <gb10>
 New blixem: improved column resizing
 blxviewMainWindow.c | 69 ++++++++++++++++++++++++++++++++++++++---------------
 detailviewtree.c    | 33 +++++++++++++++++++++----
 2 files changed, 78 insertions(+), 24 deletions(-)

2010-03-18  gb10  <gb10>
 New blixem: added basic ability to change column sizes
 blxviewMainWindow.c |  67 +++++++++++++++++++++++++++--
 detailview.c        |  96 +++++++++++++++++++++---------------------
 detailview.h        |   4 ++
 detailviewtree.c    | 118 +++++++++++++++++++++++++++++++++++++++++++++-------
 detailviewtree.h    |   9 ++--
 5 files changed, 224 insertions(+), 70 deletions(-)

2010-03-17  gb10  <gb10>
 New blixem: don't resize column headers unless necessary
 detailview.c     |  21 ++++++++--
 detailview.h     |   2 +
 detailviewtree.c | 115 +++++++++++++++++++++++++++++++++++++++----------------
 detailviewtree.h |   1 +
 4 files changed, 103 insertions(+), 36 deletions(-)

2010-03-17  gb10  <gb10>
 New blixem: got rid of global fetchMode variable
 blixem_.h           |  8 ++++----
 blxFetch.c          | 13 +++++++------
 blxdotter.c         |  9 +++++----
 blxview.c           |  4 ++--
 blxviewMainWindow.c |  6 ++++++
 blxviewMainWindow.h |  1 +
 detailviewtree.c    |  2 +-
 7 files changed, 26 insertions(+), 17 deletions(-)

2010-03-17  gb10  <gb10>
 New blixem: re-enabled printing. Misc tidy-up.
 blixem_.h           |  37 ++++++--
 blxFetch.c          | 119 +------------------------
 blxdotter.c         |  22 +++--
 blxmain.c           |   4 +-
 blxview.c           |  55 ++++++------
 blxviewMainWindow.c | 247 +++++++++++++++++++++++-----------------------------
 blxviewMainWindow.h |  32 +++----
 detailviewtree.c    |  34 +-------
 8 files changed, 204 insertions(+), 346 deletions(-)

2010-03-17  gb10  <gb10>
 New blixem: added tree gridlines
 detailviewtree.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-03-17  gb10  <gb10>
 New blixem: improved help
 blxviewMainWindow.c | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

2010-03-15  gb10  <gb10>
 New blixem: added functionality to middle-click the nucleotide header to select a nucleotide in protein matches
 detailview.c | 199 +++++++++++++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 186 insertions(+), 13 deletions(-)

2010-03-12  gb10  <gb10>
 New blixem: made grid headers show round values. Fixed some bugs with msp lines and exon boxes not lining up
 bigpicture.c     | 193 ++++++++++++++++++++++++++++++++++++++-----------------
 bigpicture.h     |   7 +-
 bigpicturegrid.c |  73 +++++++++++++--------
 detailview.c     |   8 +--
 detailviewtree.c |   2 +-
 exonview.c       |  20 +++---
 utilities.c      |  11 ++++
 utilities.h      |   1 +
 8 files changed, 210 insertions(+), 105 deletions(-)

2010-03-11  gb10  <gb10>
 New blixem: fixed uninitialised value bugs
 blxparser.c  | 11 ++++++++++-
 detailview.c |  1 +
 2 files changed, 11 insertions(+), 1 deletion(-)

2010-03-11  gb10  <gb10>
 New blixem: fixed problem with dotter getting the ref seq the wrong way round
 blxdotter.c            |  7 ++++---
 blxviewMainWindow.c    | 34 ++++++++++++++++++++++++----------
 blxviewMainWindow.h    |  1 +
 detailviewtree.c       |  2 ++
 sequencecellrenderer.c |  1 +
 5 files changed, 32 insertions(+), 13 deletions(-)

2010-03-11  gb10  <gb10>
 New blixem: removed more unnecessary code
 blxview.c           | 169 +---------------------------------------------------
 blxviewMainWindow.c |   9 +++
 2 files changed, 12 insertions(+), 166 deletions(-)

2010-03-11  gb10  <gb10>
 New blixem: general code tidying
 blxview.c           | 1702 ++++-----------------------------------------------
 blxviewMainWindow.c |    9 -
 detailview.c        |    2 +-
 detailview.h        |    1 +
 4 files changed, 138 insertions(+), 1576 deletions(-)

2010-03-11  gb10  <gb10>
 New blixem: fixed a bug where MSP lines were not being displayed if both ends extended beyond the display range
 bigpicturegrid.c | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

2010-03-10  gb10  <gb10>
 New blixem: fixed initial zoom level for big picture (used to just zoom to the whole range)
 bigpicture.c        | 42 +++++++++++++++++++++++++++++++-----------
 bigpicture.h        |  5 +++--
 blxview.c           |  8 +++++---
 blxviewMainWindow.c |  5 +++--
 blxviewMainWindow.h |  3 ++-
 detailview.c        | 18 +++++++++++++-----
 6 files changed, 57 insertions(+), 24 deletions(-)

2010-03-10  gb10  <gb10>
 New blixem: removed some unnecessary debug output
 blxviewMainWindow.c | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

2010-03-10  gb10  <gb10>
 New blixem: fixed a bug with rows disappearing when squash/unsquashing matches
 detailviewtree.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

2010-03-10  gb10  <gb10>
 New blixem: selected sequence names are now copied to primary clipboard. Also added Ctrl-C shortcut to copy sequence names to default clipboard
 blxviewMainWindow.c | 76 ++++++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 69 insertions(+), 7 deletions(-)

2010-03-09  gb10  <gb10>
 New blixem: added second exon view for reverse strand
 bigpicture.c        | 55 ++++++++++++++++++++++++++++++++++-----------
 bigpicture.h        | 30 ++++++++++++++-----------
 blxviewMainWindow.c | 64 +++++++++++++++++++++++++++++++++++++++++------------
 detailview.c        | 19 ++++++++++++----
 exonview.c          | 38 ++++++++++++++++++++++---------
 exonview.h          |  5 +++--
 6 files changed, 155 insertions(+), 56 deletions(-)

2010-03-09  gb10  <gb10>
 New blixem: made dialogs non-modal
 blixem_.h           |   4 +-
 blxFetch.c          |  58 ++++++++--------------
 blxview.c           | 139 +---------------------------------------------------
 blxviewMainWindow.c |  59 +++++-----------------
 detailviewtree.c    |   2 +-
 utilities.c         |  61 +++++++++++++++++++++++
 utilities.h         |   9 ++++
 7 files changed, 105 insertions(+), 227 deletions(-)

2010-03-09  gb10  <gb10>
 New blixem: fixed memory corruption bug where string lengths were being calculated incorrectly for negative coord values
 utilities.c | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

2010-03-09  gb10  <gb10>
 New blixem: temporarily removed some newer GTK calls to make it compatible with previous versions of GTK
 bigpicture.c        |   2 +-
 blxviewMainWindow.c | 144 ++++++++++++++++++++++++++--------------------------
 blxviewMainWindow.h |   2 +-
 detailviewtree.c    |   7 +--
 4 files changed, 78 insertions(+), 77 deletions(-)

2010-02-26  gb10  <gb10>
 Graph package replacement: fixed bug with go-to coords
 detailview.c | 57 ++++++++++++++++++++++++++++++++-------------------------
 1 file changed, 32 insertions(+), 25 deletions(-)

2010-02-26  gb10  <gb10>
 Graph package replacement: fixed small bug
 bigpicture.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-02-26  gb10  <gb10>
 Graph package replacement: misc fixes and usability improvements
 bigpicture.c           | 32 ++++++++++-------
 bigpicture.h           |  1 +
 blxviewMainWindow.c    | 39 ++++++++++++--------
 blxviewMainWindow.h    |  3 ++
 detailview.c           | 98 +++++++++++++++++++++++++++-----------------------
 detailview.h           |  8 ++---
 detailviewtree.c       | 14 ++++----
 sequencecellrenderer.c |  9 +++--
 8 files changed, 119 insertions(+), 85 deletions(-)

2010-02-25  gb10  <gb10>
 Graph package replacement: improvements to selection highlighting
 detailview.c           | 22 ++++++++--------------
 detailviewtree.c       |  4 ++--
 sequencecellrenderer.c | 34 ++++++++++------------------------
 3 files changed, 20 insertions(+), 40 deletions(-)

2010-02-25  gb10  <gb10>
 Graph package replacement: fixed a bug with exon boundary colours
 sequencecellrenderer.c | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

2010-02-24  gb10  <gb10>
 Graph package replacement: fixed bugs with selection coords when strands toggled
 detailview.c           | 15 +++++----------
 sequencecellrenderer.c | 17 +++++------------
 utilities.c            | 19 -------------------
 utilities.h            |  9 ---------
 4 files changed, 10 insertions(+), 50 deletions(-)

2010-02-24  gb10  <gb10>
 Graph package replacement: completed previous change to the way the display range works. Also improved colours.
 bigpicture.c           |  12 ++---
 bigpicturegrid.c       |  23 ++++-----
 blxdotter.c            |  11 ++++-
 blxparser.c            |   4 +-
 blxview.h              |   6 +--
 blxviewMainWindow.c    |  31 ++++--------
 blxviewMainWindow.h    |   2 -
 detailview.c           |  84 +++++++++++++++++++--------------
 detailview.h           |   1 -
 detailviewtree.c       |  14 ++----
 exonview.c             |   4 +-
 sequencecellrenderer.c |  17 ++++---
 utilities.c            | 126 ++++++++++++++++++++++++++-----------------------
 utilities.h            |  59 ++++++++++++-----------
 14 files changed, 197 insertions(+), 197 deletions(-)

2010-02-24  gb10  <gb10>
 Graph package replacement: changed the way display range works. This fixes the scroll bar being the wrong way round for reverse strand. Also fixed some issues with protein matches when the length is not an exact number of triplets. Work in progress.
 bigpicture.c           |  36 +++++-------
 bigpicture.h           |   3 +-
 bigpicturegrid.c       |  83 +++++++++++---------------
 blxdotter.c            |  12 ++--
 blxviewMainWindow.c    |  84 +++++++++++++-------------
 blxviewMainWindow.h    |  15 ++---
 detailview.c           |  90 ++++++++++++++--------------
 detailviewtree.c       | 157 +++++++++++++++++++++----------------------------
 exonview.c             |  22 +++++--
 sequencecellrenderer.c |  25 ++++----
 utilities.c            |  79 ++++++++++++++++++-------
 utilities.h            |  30 +++++++---
 12 files changed, 330 insertions(+), 306 deletions(-)

2010-02-24  gb10  <gb10>
 Graph package replacement: various bug fixes
 blxviewMainWindow.c    | 22 ++++++++++++++++++----
 blxviewMainWindow.h    |  2 +-
 detailview.c           | 13 +++----------
 detailview.h           |  2 +-
 detailviewtree.h       |  3 +--
 sequencecellrenderer.c | 18 ++++++++++++++----
 utilities.c            |  3 +++
 7 files changed, 41 insertions(+), 22 deletions(-)

2010-02-23  gb10  <gb10>
 Graph package replacement: fixed a bug with selecting a sequence that has msps in different reading frames. Added highlight colour for exons.
 detailviewtree.c |  24 ++++++-----
 exonview.c       | 119 +++++++++++++++++++++++++++++++++++++++++--------------
 2 files changed, 104 insertions(+), 39 deletions(-)

2010-02-23  gb10  <gb10>
 Graph package replacement: fixed bugs with sorting and squash matches.
 blxviewMainWindow.c | 79 ++++++++++++++++++++++++-----------------------------
 detailviewtree.c    | 52 ++++++++++++++++++++++++++++-------
 2 files changed, 77 insertions(+), 54 deletions(-)

2010-02-22  gb10  <gb10>
 Graph package replacement: added Highlight Differences option. Fixed colour of insertion marker when base is selected. Fixed a bug with exon boundary showing in wrong place.
 blxviewMainWindow.c    |  15 +++-
 blxviewMainWindow.h    |   2 +-
 detailview.c           |  27 +++++--
 detailview.h           |  12 ++-
 detailviewtree.c       |   4 +-
 detailviewtree.h       |   2 +-
 sequencecellrenderer.c | 197 ++++++++++++++++++++++++++++---------------------
 utilities.h            |   2 +-
 8 files changed, 160 insertions(+), 101 deletions(-)

2010-02-22  gb10  <gb10>
 Graph package replacement: abbreviate sequence names to fit column size and append strand and frame number
 blxview.c        |  69 +-----------------------
 detailviewtree.c | 160 +++++++++++++++++++++++++++++++++++++++++++++++++------
 utilities.c      |  38 ++++++++++++-
 utilities.h      |   1 +
 4 files changed, 183 insertions(+), 85 deletions(-)

2010-02-22  gb10  <gb10>
 Graph package replacement: added basic help
 blxviewMainWindow.c | 201 +++++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 159 insertions(+), 42 deletions(-)

2010-02-22  gb10  <gb10>
 Graph package replacement: enable middle clicking on tree headers
 detailview.c     |  74 +++++++++++++++++------------
 detailview.h     |   2 +-
 detailviewtree.c | 140 ++++++++++++++++++++++++++++++++++++++++++++++++-------
 3 files changed, 169 insertions(+), 47 deletions(-)

2010-02-19  gb10  <gb10>
 Graph package replacement: fixed bugs with sorting and start coord
 blxviewMainWindow.c | 43 +++++++++++++++++++++++++++++++------
 detailview.c        | 12 +++++++++++
 detailview.h        |  1 +
 detailviewtree.c    | 62 +++++++++++++++++++++++++++++++++--------------------
 4 files changed, 88 insertions(+), 30 deletions(-)

2010-02-19  gb10  <gb10>
 Graph package replacement: now uses input coord and offset. Fixed some issues with sorting
 bigpicturegrid.c       |   2 +-
 blixem_.h              |  12 +++--
 blxFetch.c             |  10 ++--
 blxmain.c              |  13 +++--
 blxparser.c            |   4 +-
 blxselect.c            |   7 +--
 blxview.c              |  31 +++++++----
 blxviewMainWindow.c    |  49 +++++++++++------
 blxviewMainWindow.h    |   3 ++
 detailview.c           | 141 ++++++++++++++++++++++++++++++++++---------------
 detailview.h           |  11 ++--
 detailviewtree.c       |  72 +++++++++++++++++++------
 sequencecellrenderer.c |   6 +--
 utilities.c            |  15 ++++--
 utilities.h            |   3 +-
 15 files changed, 266 insertions(+), 113 deletions(-)

2010-02-18  gb10  <gb10>
 Fixed linux 64 bug that was causing config file read to fail
 blxFetch.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

2010-02-18  gb10  <gb10>
 Graph package replacement: fixed another backwards compatibility issue
 blxviewMainWindow.c | 42 ++++++++++++++++++++++++++----------------
 1 file changed, 26 insertions(+), 16 deletions(-)

2010-02-18  gb10  <gb10>
 Graph package replacement: fixed typo
 sequencecellrenderer.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-02-18  gb10  <gb10>
 Graph package replacement: fixed incompatibilities with older versions of GTK
 bigpicturegrid.c       |   9 ----
 blxviewMainWindow.c    |  53 +++++++------------
 sequencecellrenderer.c |  15 +-----
 utilities.c            | 138 ++++++++++++++++++++++++++++++++++---------------
 4 files changed, 117 insertions(+), 98 deletions(-)

2010-02-18  gb10  <gb10>
 Graph package replacement: sorted out a bug with colours
 bigpicturegrid.c       |  7 ++++---
 blxviewMainWindow.c    | 16 +++-------------
 detailviewtree.c       | 11 +++++------
 sequencecellrenderer.c |  2 +-
 utilities.c            | 24 +++++++++++++++++++++---
 utilities.h            | 43 +++++++++++++++++++++----------------------
 6 files changed, 55 insertions(+), 48 deletions(-)

2010-02-18  gb10  <gb10>
 Graph package replacement: improved scrolling when a row is selected
 bigpicturegrid.c |  7 ++++++-
 detailviewtree.c | 18 ++++++++++++------
 detailviewtree.h |  1 +
 3 files changed, 19 insertions(+), 7 deletions(-)

2010-02-17  gb10  <gb10>
 Graph package replacement: added sort-by-group. Added group color picker.
 blxviewMainWindow.c | 113 +++++++++++++++++++++++++++++++++++++++++++++----
 blxviewMainWindow.h |   2 +
 detailview.c        |  14 ++++++
 detailview.h        |   2 +
 detailviewtree.c    | 120 +++++++++++++++++++++++++++++++++++++++-------------
 detailviewtree.h    |   2 +
 6 files changed, 215 insertions(+), 38 deletions(-)

2010-02-17  gb10  <gb10>
 Graph package replacement: added Select Features menu option. Added confirmation message for deleting groups
 blxview.c           | 922 +---------------------------------------------------
 blxviewMainWindow.c |  66 +++-
 blxviewMainWindow.h |   2 +
 3 files changed, 66 insertions(+), 924 deletions(-)

2010-02-17  gb10  <gb10>
 Graph package replacement: bug fixes with grouping and selections
 blixem_.h           |   4 +-
 blxdotter.c         |  13 ---
 blxviewMainWindow.c | 331 +++++++++++++++++++++++++++++++++++-----------------
 utilities.c         |  16 +++
 utilities.h         |   3 +
 5 files changed, 242 insertions(+), 125 deletions(-)

2010-02-16  gb10  <gb10>
 Graph package replacement: search by sequence name; hide groups
 blxparser.c         |  77 +----------
 blxview.c           |  36 +++---
 blxviewMainWindow.c | 359 +++++++++++++++++++++++++++++++++++++++++++---------
 detailview.c        |   2 +-
 detailview.h        |   1 +
 detailviewtree.c    |   9 ++
 utilities.c         |  70 ++++++++++
 utilities.h         |   1 +
 8 files changed, 397 insertions(+), 158 deletions(-)

2010-02-16  gb10  <gb10>
 Graph package replacement: small bug fix with grouping
 blixem_.h    | 15 ++++++++++++++-
 detailview.c |  2 +-
 utilities.h  |  2 ++
 3 files changed, 17 insertions(+), 2 deletions(-)

2010-02-16  gb10  <gb10>
 Graph package replacement: added basic grouping. Improved row selection.
 bigpicturegrid.c       |  26 +++++-
 blxviewMainWindow.c    | 217 ++++++++++++++++++++++++++++++++++++++++++++-----
 blxviewMainWindow.h    |   4 +
 detailview.c           |  19 ++++-
 detailview.h           |   1 +
 detailviewtree.c       |  34 ++++++--
 sequencecellrenderer.c |  26 ++++++
 7 files changed, 298 insertions(+), 29 deletions(-)

2010-02-16  gb10  <gb10>
 Graph package replacement: added subject sequence struct
 bigpicturegrid.c | 12 ++++++------
 blixem_.h        |  9 ++++++++-
 detailview.c     |  3 ++-
 detailview.h     |  2 +-
 detailviewtree.c | 30 ++++++++++++++++--------------
 utilities.c      | 22 ++++++++++++++++------
 6 files changed, 49 insertions(+), 29 deletions(-)

2010-02-15  gb10  <gb10>
 Graph package replacement: allow multiple selections
 bigpicturegrid.c    | 60 +++++++++++++++++++++++++++--------------------------
 blxdotter.c         | 56 ++++++++++++++++++++++++++++++-------------------
 blxviewMainWindow.c | 38 +++++++++++++++++++++++++--------
 detailview.c        | 20 +++++++++++-------
 detailview.h        |  5 +++--
 5 files changed, 110 insertions(+), 69 deletions(-)

2010-02-15  gb10  <gb10>
 Graph package replacement: improved performance of grid preview box by drawing grid to pixmap. Also added pfetch.
 bigpicture.c        | 114 +++++++++++++++++++++++++++++++++++++---------------
 bigpicture.h        |   5 +--
 bigpicturegrid.c    |  85 ++++++++++++++++++++-------------------
 bigpicturegrid.h    |   3 --
 blixem_.h           |   4 +-
 blxFetch.c          |  71 +++++++++++++++++++++++---------
 blxdotter.c         |   2 +-
 blxviewMainWindow.c |  17 ++++++--
 blxviewMainWindow.h |   2 +
 detailview.c        |  72 +++++++++++++--------------------
 detailview.h        |   2 +-
 detailviewtree.c    |  47 +++++++++++++++-------
 utilities.c         |  26 +++++++++++-
 utilities.h         |   2 +
 14 files changed, 288 insertions(+), 164 deletions(-)

2010-02-11  gb10  <gb10>
 Graph package replacement: bug fixes. Fixed scrolling on linux. Fixed missing grid header. Fixed prev/next match for protein matches.
 bigpicture.c           |  22 +++++-----
 bigpicturegrid.c       | 111 +++++++++++++++++++++++++------------------------
 bigpicturegrid.h       |   2 +-
 blxdotter.c            |   4 +-
 blxviewMainWindow.c    |  17 ++++----
 detailview.c           |  28 +++++++------
 detailviewtree.c       |  44 +++++++++++---------
 exonview.c             |   5 +--
 sequencecellrenderer.c |   6 +--
 utilities.c            |  52 ++++++++++++++++++-----
 utilities.h            |   2 +
 11 files changed, 168 insertions(+), 125 deletions(-)

2010-02-10  gb10  <gb10>
 Graph package replacement: fixed bug where s index was not being shown for protein matches
 detailview.c | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

2010-02-10  gb10  <gb10>
 Graph package replacement: squash matches now working
 bigpicturegrid.c    | 101 +++++++++++++++++++++++++++++--------------------
 blxdotter.c         |  70 ++++++++++++++++++++--------------
 blxviewMainWindow.c | 100 +++++++++++++++++++++++++++++++++++++------------
 blxviewMainWindow.h |  13 ++++---
 detailview.c        |  94 ++++++++++++++++++++++++++++++++--------------
 detailview.h        |   4 +-
 detailviewtree.c    | 106 +++++++++++++++++++++++-----------------------------
 detailviewtree.h    |   8 ++--
 utilities.c         |  12 +++++-
 utilities.h         |   2 +
 10 files changed, 317 insertions(+), 193 deletions(-)

2010-02-10  gb10  <gb10>
 Graph package replacement: squash matches
 detailview.c     |   2 +
 detailviewtree.c | 135 ++++++++++++++++++++++++++++++++++++++++++-------------
 detailviewtree.h |   4 +-
 3 files changed, 108 insertions(+), 33 deletions(-)

2010-02-09  gb10  <gb10>
 Graph package replacement: further small performance improvement
 sequencecellrenderer.c | 59 +++++++++++++++++++++++++++-----------------------
 1 file changed, 32 insertions(+), 27 deletions(-)

2010-02-09  gb10  <gb10>
 Graph package replacement: improved speed of squash-matches view
 sequencecellrenderer.c | 203 ++++++++++++++++++++-----------------------------
 1 file changed, 84 insertions(+), 119 deletions(-)

2010-02-09  gb10  <gb10>
 Graph package replacement: squash matches (work in progress). Also added (mostly empty) settings dialog.
 bigpicture.c           |  14 +++
 bigpicture.h           |   2 +
 blxviewMainWindow.c    | 138 ++++++++++++++++++++---------
 detailview.c           |  27 +++++-
 detailview.h           |   3 +
 detailviewtree.c       |  63 ++++++++++---
 detailviewtree.h       |   7 ++
 sequencecellrenderer.c | 235 +++++++++++++++++++++++++++++--------------------
 8 files changed, 339 insertions(+), 150 deletions(-)

2010-02-09  gb10  <gb10>
 Graph package replacement: squash matches (work in progress)
 detailview.c     |  2 ++
 detailviewtree.c | 24 +++++++++++++++---------
 detailviewtree.h |  1 +
 3 files changed, 18 insertions(+), 9 deletions(-)

2010-02-09  gb10  <gb10>
 Graph package replacement: fixed a couple of bugs with scrolling and row selections
 detailview.c     |  53 ++++++++++++++++++++------
 detailviewtree.c | 112 ++++++++++++++++++++++++++++++++++++++++++++++---------
 detailviewtree.h |   5 +--
 3 files changed, 139 insertions(+), 31 deletions(-)

2010-02-08  gb10  <gb10>
 Graph package replacement: work in progress: squash matches
 bigpicturegrid.c       |  57 ++++++++----
 blxviewMainWindow.c    |  16 ++--
 blxviewMainWindow.h    |   8 +-
 detailview.c           |  73 +++++++--------
 detailview.h           |   2 +-
 detailviewtree.c       | 235 ++++++++++++++++++++++---------------------------
 detailviewtree.h       |   4 +-
 exonview.c             |  58 ++++++------
 sequencecellrenderer.c | 114 ++++++++++++------------
 sequencecellrenderer.h |   4 +-
 10 files changed, 287 insertions(+), 284 deletions(-)

2010-02-08  gb10  <gb10>
 Graph package replacement: small improvement to middle-mouse scrolling
 detailviewtree.c | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

2010-02-08  gb10  <gb10>
 Graph package replacement: highlight selected triplet for protein matches
 blxviewMainWindow.c |  84 ++++++++++++++++++---------
 detailview.c        | 161 +++++++++++++++++++++++++++++++++++++++++++---------
 detailview.h        |   9 ++-
 detailviewtree.c    | 153 +++++++++++++++++++++++++++++--------------------
 utilities.h         |   3 +-
 5 files changed, 295 insertions(+), 115 deletions(-)

2010-02-05  gb10  <gb10>
 Graph package replacement: fixed small bugs with hiding windows
 blxviewMainWindow.c | 85 +++++++++++++++++++++++++++++++++++++++++++----------
 detailview.c        | 39 +++++++++++++++++++++++-
 detailview.h        |  1 +
 3 files changed, 108 insertions(+), 17 deletions(-)

2010-02-05  gb10  <gb10>
 Graph package replacement: Fixed bug with exon end coords being one off for frames 2 and 3. Added shortcut key to hide panes. Fixed a bug where scroll range refresh wasn't happening if frame 1 was hidden.
 bigpicturegrid.c       |  19 ++----
 blxviewMainWindow.c    |  66 +++++++++++++++---
 detailview.c           | 109 +++++++++++++++--------------
 detailviewtree.c       |   6 +-
 sequencecellrenderer.c | 138 +------------------------------------
 sequencecellrenderer.h |   2 -
 utilities.c            | 182 +++++++++++++++++++++++++++++++++++++++++++++++--
 utilities.h            |  20 +++++-
 8 files changed, 319 insertions(+), 223 deletions(-)

2010-02-04  gb10  <gb10>
 Graph package replacement: fixed a few bugs with starting dotter
 blxdotter.c | 2 +-
 dotter.c    | 4 ++--
 utilities.c | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

2010-02-04  gb10  <gb10>
 Graph package replacement: added dotter settings dialog
 blxdotter.c         | 825 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 blxdotter.h         |  24 ++
 blxviewMainWindow.c |  20 +-
 blxviewMainWindow.h |   4 +
 detailview.c        |   1 +
 detailview.h        |   2 +-
 6 files changed, 869 insertions(+), 7 deletions(-)

2010-02-04  gb10  <gb10>
 Graph package replacement: added ability to call dotter
 blxmain.c              |  53 ++---
 blxview.c              | 632 +------------------------------------------------
 blxviewMainWindow.c    | 104 +++++---
 blxviewMainWindow.h    |  37 ++-
 detailviewtree.c       |  17 +-
 dotter.c               |  36 +--
 dotter.h               |  10 +-
 dotter_.h              |   9 +-
 sequencecellrenderer.c |  13 +-
 utilities.c            |  32 ++-
 utilities.h            |   7 +-
 11 files changed, 212 insertions(+), 738 deletions(-)

2010-02-03  gb10  <gb10>
 Graph package replacement: added ability to show/hide panes
 bigpicture.c        |   7 +-
 bigpicture.h        |   3 +-
 bigpicturegrid.c    |   6 +-
 blxview.c           |  27 +----
 blxviewMainWindow.c | 328 ++++++++++++++++++++++++++++++++++++++++------------
 blxviewMainWindow.h |   4 +-
 detailview.c        |  98 +++++++++++-----
 detailview.h        |   5 +-
 detailviewtree.c    |   9 +-
 exonview.c          |   4 +-
 utilities.c         |  54 +++++++--
 utilities.h         |   2 +
 12 files changed, 394 insertions(+), 153 deletions(-)

2010-02-02  gb10  <gb10>
 Graph package replacement: highlight colour for similar peptide matches added
 detailview.c           |  8 ++++++++
 detailview.h           |  3 +++
 detailviewtree.c       | 26 +++++++++++++++++++++++---
 detailviewtree.h       |  5 ++++-
 iupac.h                |  9 ++++++++-
 sequencecellrenderer.c | 23 ++++++++++++++---------
 utilities.h            | 31 +++++++++++++++++--------------
 7 files changed, 77 insertions(+), 28 deletions(-)

2010-02-02  gb10  <gb10>
 Graph package replacement: Made protein matches display correctly when strands toggled.
 bigpicture.c           |  4 ++-
 bigpicturegrid.c       |  4 +--
 blxviewMainWindow.c    |  4 +--
 detailview.c           | 70 ++++++++++++++++++++++++++++----------------------
 detailview.h           | 10 +++++---
 detailviewtree.c       | 26 +++++++++++++------
 detailviewtree.h       |  4 +--
 sequencecellrenderer.c | 13 +++++++---
 utilities.c            | 22 ++++++++--------
 utilities.h            |  9 +++++--
 10 files changed, 101 insertions(+), 65 deletions(-)

2010-02-01  gb10  <gb10>
 Graph package replacement: now draws exon boundaries in all rows in tree view
 detailview.c           | 22 +++++++++++++++
 detailview.h           | 29 +++++++++++--------
 detailviewtree.c       | 26 ++++++++++++++---
 detailviewtree.h       |  3 ++
 sequencecellrenderer.c | 76 +++++++++++++++++++++++++++++++++++++++++++++++++-
 5 files changed, 140 insertions(+), 16 deletions(-)

2010-01-29  gb10  <gb10>
 Graph package replacement: jump to next/prev match
 bigpicturegrid.c    |  14 ++-
 blxview.c           |  53 +---------
 blxviewMainWindow.c |  19 ++--
 detailview.c        | 281 +++++++++++++++++++++++++++++++++++++++-------------
 detailview.h        |   3 +-
 detailviewtree.c    |  16 +--
 utilities.c         |   9 +-
 utilities.h         |   3 +-
 8 files changed, 253 insertions(+), 145 deletions(-)

2010-01-29  gb10  <gb10>
 Graph package replacement: key shortcuts for scrolling and zooming
 bigpicture.c        |  31 ++++++----
 bigpicture.h        |   1 +
 blxviewMainWindow.c | 168 ++++++++++++++++++++++++++++++++++++----------------
 detailview.c        |  64 ++++++++++----------
 detailview.h        |   1 +
 5 files changed, 172 insertions(+), 93 deletions(-)

2010-01-29  gb10  <gb10>
 Graph package replacement: added printing support
 bigpicture.c           |  15 ++++++++
 bigpicturegrid.c       |  43 +++++++--------------
 bigpicturegrid.h       |   1 -
 blxviewMainWindow.c    | 102 ++++++++++++++++++++++++++++---------------------
 blxviewMainWindow.h    |   4 ++
 detailview.c           |  13 +------
 detailviewtree.c       |  53 +++++++++----------------
 detailviewtree.h       |   2 -
 exonview.c             |  23 +++++++++--
 sequencecellrenderer.c |  12 +++---
 utilities.c            |  93 +++++++++++++++++++++++++++++++++++++++++++-
 utilities.h            |   6 +++
 12 files changed, 232 insertions(+), 135 deletions(-)

2010-01-28  gb10  <gb10>
 Graph package replacement: printing - work in progress
 blxviewMainWindow.c    | 44 +++++++++++++++++++++-----
 detailviewtree.c       | 32 +++++++++++++++++++
 detailviewtree.h       | 16 +++++-----
 sequencecellrenderer.c | 84 ++++++++++++++++++++++++++++++++++++++------------
 4 files changed, 142 insertions(+), 34 deletions(-)

2010-01-28  gb10  <gb10>
 Graph package replacements: refactored SequenceCellRenderer code
 detailview.c           |  85 ++++++-------
 detailview.h           |  31 ++---
 detailviewtree.c       | 135 +++++++++------------
 detailviewtree.h       |  13 +-
 sequencecellrenderer.c | 324 +++++++++++++++++++------------------------------
 sequencecellrenderer.h |   7 --
 6 files changed, 247 insertions(+), 348 deletions(-)

2010-01-28  gb10  <gb10>
 Graph package replacement: started adding printing support
 blxviewMainWindow.c | 131 ++++++++++++++++++++++++++++++++++++++++++++++++----
 blxviewMainWindow.h |   4 +-
 detailview.c        |   2 +-
 detailview.h        |   1 +
 utilities.h         |   1 +
 5 files changed, 128 insertions(+), 11 deletions(-)

2010-01-27  gb10  <gb10>
 Graph package replacement: draw grid to pixmap rather than straight to screen.
 bigpicture.c        |   6 ++
 bigpicturegrid.c    | 211 +++++++++++++++++++++++++++++++++++-----------------
 bigpicturegrid.h    |   5 ++
 blxviewMainWindow.c |   9 ++-
 detailview.c        |  61 +++++----------
 detailviewtree.c    |  12 ---
 detailviewtree.h    |   1 -
 7 files changed, 177 insertions(+), 128 deletions(-)

2010-01-26  gb10  <gb10>
 Graph package replacement: improvements to scrolling and to make tree row sizing more robust.
 detailview.c           | 73 +++++++++++++++++++++++++------------
 detailview.h           |  8 ++---
 detailviewtree.c       | 10 ++++--
 sequencecellrenderer.c | 98 +++++++++++++++++++++++++-------------------------
 sequencecellrenderer.h |  1 +
 5 files changed, 112 insertions(+), 78 deletions(-)

2010-01-25  gb10  <gb10>
 Graph package replacement: allow selection of MSPs that are not in the filtered tree
 bigpicturegrid.c       |  61 ++--
 blxview.c              |   4 +-
 blxview.h              |   4 +-
 blxviewMainWindow.c    | 169 ++++++++----
 blxviewMainWindow.h    |   8 +
 detailview.c           | 180 +++++++++---
 detailview.h           |   3 +-
 detailviewtree.c       | 737 ++++++++++++++++++++++++-------------------------
 detailviewtree.h       |  10 +-
 sequencecellrenderer.c | 131 ++-------
 utilities.c            |   8 -
 utilities.h            |   1 -
 12 files changed, 695 insertions(+), 621 deletions(-)

2010-01-22  gb10  <gb10>
 Graph package replacement: added separate tree view headers
 bigpicturegrid.c       |   2 +-
 blxviewMainWindow.c    |   3 +
 detailview.c           | 414 +++++++++++++++++++++++++++----------------------
 detailview.h           |  75 +++++++--
 detailviewtree.c       | 373 ++++++++++++++++++++++++++++++++++++--------
 detailviewtree.h       |  31 ++--
 sequencecellrenderer.c |  24 +--
 utilities.c            |  43 +++++
 utilities.h            |  14 +-
 9 files changed, 690 insertions(+), 289 deletions(-)

2010-01-21  gb10  <gb10>
 Graph package replacement: fixed issue with tiny MSP lines not showing. Fixed CalcId for reverse strand
 bigpicturegrid.c |  37 ++++++++++++-------
 detailviewtree.c | 109 ++++++++++++++++++-------------------------------------
 2 files changed, 58 insertions(+), 88 deletions(-)

2010-01-21  gb10  <gb10>
 Graph package replacement: fixed exon positions for protain matches. Fixed highlighting.
 bigpicturegrid.h       |  2 --
 detailview.c           | 18 +++++++++++++++-
 detailviewtree.c       | 18 ++++++++++++----
 exonview.c             |  4 ++--
 sequencecellrenderer.c | 58 ++++++++++++++++++++++++++++++++++++++++++++++----
 sequencecellrenderer.h |  2 --
 utilities.c            |  9 ++++++++
 utilities.h            |  4 ++++
 8 files changed, 100 insertions(+), 15 deletions(-)

2010-01-21  gb10  <gb10>
 Graph package replacement: always show coords in terms of the DNA sequence.
 blxviewMainWindow.c    |  6 +++---
 detailview.h           |  4 ++--
 detailviewtree.c       | 38 +++++++++++++++++++++++++++++++++++---
 sequencecellrenderer.c |  3 ++-
 4 files changed, 42 insertions(+), 9 deletions(-)

2010-01-21  gb10  <gb10>
 Graph package replacement: fixed big picture grid view for protein matches
 bigpicture.c           |   6 +--
 bigpicture.h           |   3 ++
 bigpicturegrid.c       | 119 +++++++++++++++++++++++++++++++------------------
 bigpicturegrid.h       |   1 -
 detailview.c           |  83 ++++++++++++++++------------------
 detailview.h           |   3 +-
 detailviewtree.c       |   7 ++-
 exonview.c             |   4 +-
 sequencecellrenderer.c |  10 +----
 9 files changed, 127 insertions(+), 109 deletions(-)

2010-01-20  gb10  <gb10>
 Graph package replacement: calcId fixes
 blxviewMainWindow.c    | 21 ++++++++--------
 blxviewMainWindow.h    |  4 +++-
 detailview.c           | 14 ++++++-----
 detailviewtree.c       | 65 +++++++++++++++++++++++++++++++++-----------------
 detailviewtree.h       |  5 ++--
 sequencecellrenderer.c | 36 +++++++++++++++-------------
 6 files changed, 87 insertions(+), 58 deletions(-)

2010-01-20  gb10  <gb10>
 Graph package replacement: initial work on protein matches.
 bigpicture.c           |   44 +-
 bigpicture.h           |    5 +-
 bigpicturegrid.c       |    5 +-
 blxFetch.c             |   72 +-
 blxmain.c              |  124 +-
 blxparser.c            |   98 +-
 blxselect.c            |    6 +-
 blxview.c              | 3137 ++++++++++++++++++++++--------------------------
 blxview.h              |   10 +-
 blxviewMainWindow.c    |  226 +++-
 blxviewMainWindow.h    |   36 +-
 detailview.c           |  169 ++-
 detailview.h           |   11 +-
 detailviewtree.c       |  143 ++-
 exonview.c             |    2 +
 sequencecellrenderer.c |  641 ++++++----
 translate.c            |    6 +-
 utilities.c            |   73 +-
 utilities.h            |   12 +-
 19 files changed, 2605 insertions(+), 2215 deletions(-)

2010-01-14  gb10  <gb10>
 Graph package replacement: Started adding handling for protein matches. Improved scrolling and navigation.
 bigpicture.c           |   3 +-
 bigpicture.h           |   1 +
 blxparser.c            |  10 +-
 blxview.c              |   4 +-
 blxviewMainWindow.c    |  64 ++++-
 blxviewMainWindow.h    |   2 +-
 detailview.c           | 732 ++++++++++++++++++++++++++++++++++++++++++++-----
 detailview.h           |  62 ++++-
 detailviewtree.c       | 479 +++++++++++---------------------
 detailviewtree.h       |  37 +--
 sequencecellrenderer.c | 270 +++++++++++++-----
 sequencecellrenderer.h |  15 +-
 12 files changed, 1172 insertions(+), 507 deletions(-)

2010-01-05  gb10  <gb10>
 Graph package replacement: added missing include.
 exonview.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

2010-01-05  gb10  <gb10>
 Graph package replacement: Fixed bug where bases were offset incorrectly when strands toggled. Added utilities file.
 bigpicture.c           |  42 +++++++------------
 bigpicturegrid.c       |  27 ++++++++----
 blixem_.h              |  26 +-----------
 blxparser.c            |  15 +------
 blxview.c              |  40 +-----------------
 blxviewMainWindow.c    |   2 +-
 detailview.c           |  35 ++++++----------
 detailviewtree.c       |  93 +++++++++++++++++++++-------------------
 detailviewtree.h       |   1 +
 sequencecellrenderer.c |   8 ++--
 utilities.c            | 112 +++++++++++++++++++++++++++++++++++++++++++++++++
 utilities.h            |  37 ++++++++++++++++
 12 files changed, 257 insertions(+), 181 deletions(-)

2010-01-05  gb10  <gb10>
 Graph package replacement: made big picture scrolling more predictable.
 bigpicture.c     | 32 ++++++++++++++++++++++++++++++--
 bigpicture.h     |  7 +++++++
 bigpicturegrid.c | 35 +++++++++++++++++++++++++----------
 3 files changed, 62 insertions(+), 12 deletions(-)

2010-01-05  gb10  <gb10>
 Graph package replacement: Detail view keeps centred on selected base when zoom. Middle-click added for exon view.
 bigpicture.c           | 23 ++++++++++++
 bigpicturegrid.c       | 95 ++++++++++++++++++++++----------------------------
 bigpicturegrid.h       |  3 ++
 detailview.c           | 65 ++++++++++++++++++++++------------
 exonview.c             | 74 +++++++++++++++++++++++++++++++++++++--
 sequencecellrenderer.c |  2 +-
 6 files changed, 181 insertions(+), 81 deletions(-)

2010-01-04  gb10  <gb10>
 Graph package replacement: implemented sorting.
 blxview.c        | 110 +++--------------
 detailview.c     | 104 ++++++++++------
 detailviewtree.c | 356 ++++++++++++++++++++++++++++++++++++++-----------------
 detailviewtree.h |   4 +
 exonview.c       |   2 -
 5 files changed, 338 insertions(+), 238 deletions(-)

2010-01-04  gb10  <gb10>
 Graph package replacement: Draw introns.
 detailviewtree.c | 74 ++++++++++++++++++++++++++------------------------------
 exonview.c       | 57 +++++++++++++++++++++++++++++++------------
 2 files changed, 76 insertions(+), 55 deletions(-)

2010-01-04  gb10  <gb10>
 Graph package replacement: removed duff dependencies.
 blxviewMainWindow.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

2010-01-04  gb10  <gb10>
 Graph package replacement: added exon view.
 exonview.c | 204 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 exonview.h |  12 ++++
 2 files changed, 216 insertions(+)

2010-01-04  gb10  <gb10>
 Graph package replacement: Added exon view. Improved scrolling.
 bigpicture.c        | 228 +++++++++++++++++++++++++++++++++++++++++++++++-----
 bigpicture.h        |  14 +++-
 bigpicturegrid.c    |  90 ++++++++++-----------
 bigpicturegrid.h    |   7 --
 blxmain.c           |  30 +++----
 blxview.c           |  11 +--
 blxviewMainWindow.c |   7 +-
 detailview.c        | 138 +++++++++++++++++++++----------
 detailview.h        |   9 ++-
 detailviewtree.c    | 114 ++++++++++++++++++--------
 10 files changed, 469 insertions(+), 179 deletions(-)

2009-12-18  gb10  <gb10>
 Graph package replacement: added functionality to select msps from the grid.
 bigpicturegrid.c | 106 +++++++++++++++++++++++++++++++++++++++++++++++++------
 detailviewtree.c |  50 ++++++++++++++++++++------
 detailviewtree.h |   3 ++
 3 files changed, 137 insertions(+), 22 deletions(-)

2009-12-18  gb10  <gb10>
 Graph package replacement: fixed bug with scrolling from big picture when strands are toggled
 bigpicturegrid.c | 29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

2009-12-18  gb10  <gb10>
 Graph package replacement: fixed coord feedback for out-of-range bases
 detailviewtree.c       |  9 ++++-
 sequencecellrenderer.c | 94 +++++++++++++++++++++++++++++++++-----------------
 sequencecellrenderer.h |  2 +-
 3 files changed, 72 insertions(+), 33 deletions(-)

2009-12-18  gb10  <gb10>
 Graph package removal: now draws gaps in the reference sequence. Also added right-click menu.
 bigpicture.c           |   3 +-
 bigpicture.h           |   3 +-
 blxviewMainWindow.c    | 257 +++++++++++++++++++++++++++++++++++++++++++++++--
 blxviewMainWindow.h    |  10 +-
 detailview.c           | 115 ++++++----------------
 detailview.h           |   3 +-
 sequencecellrenderer.c | 107 +++++++++++++++-----
 7 files changed, 373 insertions(+), 125 deletions(-)

2009-12-15  gb10  <gb10>
 Graph package replacement: fixed issue getting monospace font
 bigpicturegrid.c       |   2 +-
 blixem_.h              |   6 +-
 blxview.c              |  43 +++++---
 blxview.h              |   7 +-
 blxviewMainWindow.c    |  19 +++-
 blxviewMainWindow.h    |   5 +-
 detailview.c           | 166 ++++++++++++++++++++++--------
 detailview.h           |   9 +-
 detailviewtree.c       | 268 ++++++++++++++++++++++++++++++++++++++++++++-----
 detailviewtree.h       |  13 ++-
 sequencecellrenderer.c |  14 ++-
 11 files changed, 452 insertions(+), 100 deletions(-)

2009-12-14  gb10  <gb10>
 Graph package removal: Improved speed of setting feedback-box text. Don't draw introns or the ref sequence in the grid.
 bigpicturegrid.c       |  55 ++++++++++++----------
 blixem_.h              |   7 ++-
 detailviewtree.c       | 123 ++++++++++++++++++++++++++++++++-----------------
 sequencecellrenderer.c |  10 ++--
 4 files changed, 122 insertions(+), 73 deletions(-)

2009-12-14  gb10  <gb10>
 Graph package replacement: fixed bug where msp lines were shown incorrectly when strands are toggled.
 bigpicture.c           | 102 ++++++++++++-------------
 bigpicture.h           |  16 ++--
 bigpicturegrid.c       | 196 ++++++++++++++++++++++++++++++++++++-------------
 bigpicturegrid.h       |  19 ++++-
 blixem_.h              |  16 +++-
 blxviewMainWindow.c    |   3 -
 detailview.c           |   6 ++
 detailviewtree.c       |  79 ++++++++++++++++++++
 detailviewtree.h       |  25 +++++++
 sequencecellrenderer.c |  62 +++++++++-------
 10 files changed, 384 insertions(+), 140 deletions(-)

2009-12-11  gb10  <gb10>
 Graph package replacement: display right-to-left when strands are toggled
 bigpicture.c           |  2 +-
 bigpicturegrid.c       | 10 +++++-
 blixem_.h              |  4 ++-
 detailview.c           | 24 +++++++++++---
 detailview.h           |  3 +-
 detailviewtree.c       | 82 ++++++++++++++++++++++++++++++++++++++++++-----
 detailviewtree.h       |  2 ++
 sequencecellrenderer.c | 87 +++++++++++++++++++++++++++++++++++++++-----------
 8 files changed, 179 insertions(+), 35 deletions(-)

2009-12-10  gb10  <gb10>
 Graph package replacement: improvements to feedback box
 detailview.c     |  14 +++++-
 detailview.h     |   3 ++
 detailviewtree.c | 140 +++++++++++++++++++++++++++++++++++++++----------------
 3 files changed, 117 insertions(+), 40 deletions(-)

2009-12-10  gb10  <gb10>
 Graph package replacement: Added facility to toggle strands. Also changed cell renderer to draw the colours for sequences manually and draw the text as a single, non-marked-up pango layout (improves speed).
 bigpicture.c           |  99 +++++++-
 bigpicture.h           |  11 +-
 bigpicturegrid.c       |  33 ++-
 blxparser.c            |   4 +-
 blxview.c              |   4 +-
 blxview.h              |   6 +-
 blxviewMainWindow.c    |  31 ++-
 blxviewMainWindow.h    |  13 +-
 detailview.c           | 478 +++++++++++++++++++++++++++++---------
 detailview.h           |  18 +-
 detailviewtree.c       | 234 ++++++++-----------
 detailviewtree.h       |  13 +-
 sequencecellrenderer.c | 604 +++++++++++++++++++------------------------------
 13 files changed, 893 insertions(+), 655 deletions(-)

2009-12-08  gb10  <gb10>
 Graph package replacement: added support for exons in the detail view.
 blixem_.h              |  3 ++-
 detailviewtree.c       | 50 ++++++++++++++++++++++----------------------
 sequencecellrenderer.c | 56 +++++++++++++++++++++++++++++---------------------
 3 files changed, 60 insertions(+), 49 deletions(-)

2009-12-08  gb10  <gb10>
 Graph package replacement: forward and reverse strands both now working.
 bigpicturegrid.c       |   34 +-
 bigpicturegrid.h       |    4 +-
 blixem_.h              |   11 +-
 blxFetch.c             |  173 ++++++-
 blxmain.c              |    3 +-
 blxparser.c            |  111 ++---
 blxselect.c            |    4 +-
 blxview.c              | 1260 +++++++++++++++++++++++++-----------------------
 blxviewMainWindow.c    |    2 +-
 blxviewMainWindow.h    |    2 +-
 detailview.c           |  132 +++--
 detailview.h           |    2 +
 detailviewtree.c       |  310 +++++++++---
 detailviewtree.h       |   11 +-
 dotter.c               |    4 +-
 dotter.h               |    4 +-
 dotterMain.c           |    4 +-
 sequencecellrenderer.c |  663 ++++++++++++++++---------
 sequencecellrenderer.h |    8 +-
 translate.c            |   69 +--
 20 files changed, 1654 insertions(+), 1157 deletions(-)

2009-12-02  gb10  <gb10>
 Initial stages of Graph package replacement
 bigpicture.c           | 367 ++++++++++++++++++++++
 bigpicture.h           |  70 +++++
 bigpicturegrid.c       | 604 ++++++++++++++++++++++++++++++++++++
 bigpicturegrid.h       |  61 ++++
 blxviewMainWindow.c    | 134 ++++++++
 blxviewMainWindow.h    |  29 ++
 detailview.c           | 773 ++++++++++++++++++++++++++++++++++++++++++++++
 detailview.h           |  54 ++++
 detailviewtree.c       | 814 +++++++++++++++++++++++++++++++++++++++++++++++++
 detailviewtree.h       |  67 ++++
 sequencecellrenderer.c | 703 ++++++++++++++++++++++++++++++++++++++++++
 sequencecellrenderer.h |  58 ++++
 12 files changed, 3734 insertions(+)

2009-12-02  gb10  <gb10>
 Initial stages of Graph package removal
 blixem_.h   |   13 +-
 blxFetch.c  |   28 +-
 blxmain.c   |   24 +-
 blxview.c   | 3737 ++++++++++++++++++++++++++---------------------------------
 blxview.h   |   19 +-
 dotter.h    |    4 +-
 translate.c |    4 +-
 7 files changed, 1708 insertions(+), 2121 deletions(-)

2009-11-03  edgrif  <edgrif>
 first version of new seqtools code, copied from w9
 align.c        |  452 +++
 asn.c          | 2352 ++++++++++++++++
 belvu.c        | 8590 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 blixem_.h      |  239 ++
 blxFetch.c     | 1701 +++++++++++
 blxmain.c      |  448 +++
 blxparser.c    | 1452 ++++++++++
 blxselect.c    |  404 +++
 blxview.c      | 5495 ++++++++++++++++++++++++++++++++++++
 blxview.h      |  147 +
 dbidx.c        |  750 +++++
 diskdump.c     |  114 +
 diskfix.c      |   91 +
 dotter.c       | 4086 +++++++++++++++++++++++++++
 dotter.h       |  110 +
 dotterKarlin.c |  455 +++
 dotterMain.c   |  555 ++++
 dotter_.h      |   69 +
 efetch.c       |  533 ++++
 embl.c         | 1992 +++++++++++++
 fetch.c        |  500 ++++
 gfcode.c       | 1259 +++++++++
 hexcode.c      |  401 +++
 iupac.h        |  287 ++
 readseq.c      |  361 +++
 translate.c    |  369 +++
 vmapdata2.c    | 1895 +++++++++++++
 vmapphys.c     |  417 +++
 28 files changed, 35524 insertions(+)
