gmungoc [Thu, 3 Sep 2015 10:37:28 +0000 (11:37 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 3 Sep 2015 10:37:16 +0000 (11:37 +0100)]
JAL-1690 scaleProteinAsCdna new optional attribute on Viewport in
project file
tcofoegbu [Thu, 3 Sep 2015 10:33:47 +0000 (11:33 +0100)]
merge
tcofoegbu [Thu, 3 Sep 2015 10:27:46 +0000 (11:27 +0100)]
JAL-793 use default custom export settings for html exports
gmungoc [Thu, 3 Sep 2015 09:22:15 +0000 (10:22 +0100)]
JAL-1828 lookup table to convert MSE to MET when parsing PDB data
gmungoc [Thu, 3 Sep 2015 09:21:01 +0000 (10:21 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Wed, 2 Sep 2015 18:55:13 +0000 (19:55 +0100)]
JAL-1835 updated documentation in preferences
tcofoegbu [Wed, 2 Sep 2015 16:45:24 +0000 (17:45 +0100)]
JAL-1740 migrated BioJSMSAViewer git repo to https://github.com/jalview/exporter-templates/tree/master/biojs
tcofoegbu [Wed, 2 Sep 2015 15:50:52 +0000 (16:50 +0100)]
merge
tcofoegbu [Wed, 2 Sep 2015 15:48:07 +0000 (16:48 +0100)]
JAL-1805 JAL-1700 house keeping
tcofoegbu [Wed, 2 Sep 2015 15:44:25 +0000 (16:44 +0100)]
JAL-1739 reverted BioJSON schema to use one main version for the whole schema and remove every other versioning for different fragments of the schema
gmungoc [Wed, 2 Sep 2015 15:34:56 +0000 (16:34 +0100)]
JAL-1544 spelling
gmungoc [Wed, 2 Sep 2015 15:34:24 +0000 (16:34 +0100)]
JAL-1355 User error text externalised to message bundle
gmungoc [Wed, 2 Sep 2015 15:31:43 +0000 (16:31 +0100)]
JAL-1768 set initial 'enabled' state for id width label as well
gmungoc [Wed, 2 Sep 2015 15:27:56 +0000 (16:27 +0100)]
JAL-1264 test made i18n robust
gmungoc [Wed, 2 Sep 2015 15:21:55 +0000 (16:21 +0100)]
JAL-1768 enable fixed width output when auto-width _not_ enabled
gmungoc [Wed, 2 Sep 2015 14:55:17 +0000 (15:55 +0100)]
JAL-1843 fixed input/add from textbox; added @Override to Desktop
gmungoc [Wed, 2 Sep 2015 12:40:32 +0000 (13:40 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Wed, 2 Sep 2015 12:15:52 +0000 (13:15 +0100)]
merge
tcofoegbu [Wed, 2 Sep 2015 12:14:00 +0000 (13:14 +0100)]
JAL-1805 JAL-1782 added a draft documentation for TestNG to jalview doc directory
Jim Procter [Wed, 2 Sep 2015 11:40:14 +0000 (12:40 +0100)]
JAL-1853 add test to list for ant task
gmungoc [Wed, 2 Sep 2015 11:10:01 +0000 (12:10 +0100)]
JAL-1619 additions, standardised menu item symbols
gmungoc [Wed, 2 Sep 2015 11:08:47 +0000 (12:08 +0100)]
JAL-1681 mention of cDNA consensus added
Jim Procter [Wed, 2 Sep 2015 10:59:53 +0000 (11:59 +0100)]
JAL-535 todo: refactor logic to desktop controller class
Jim Procter [Wed, 2 Sep 2015 10:58:05 +0000 (11:58 +0100)]
JAL-1772 non-functional test added. not doing any more work for 2.9 release
gmungoc [Wed, 2 Sep 2015 10:11:32 +0000 (11:11 +0100)]
JAL-1673 new test to verify transferRESNUMFeatures()
gmungoc [Wed, 2 Sep 2015 08:27:10 +0000 (09:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Tue, 1 Sep 2015 16:40:17 +0000 (17:40 +0100)]
Merge branch 'bug/JAL-1853_gapchar_output' into develop
Jim Procter [Tue, 1 Sep 2015 16:39:15 +0000 (17:39 +0100)]
JAL-1853 add test to Functional group
Jim Procter [Tue, 1 Sep 2015 16:20:13 +0000 (17:20 +0100)]
JAL-1853 make getVisibleSeqs more memory efficient by clipping sequences as the sequence vector is populated
Jim Procter [Tue, 1 Sep 2015 16:19:38 +0000 (17:19 +0100)]
JAL-1853 refactor clip routine from getSequenceStrings
Jim Procter [Tue, 1 Sep 2015 16:15:21 +0000 (17:15 +0100)]
patch for JAL-1853 - use given gap character to reconstruct alignment
Jim Procter [Tue, 1 Sep 2015 16:10:01 +0000 (17:10 +0100)]
JAL-1853 test origin of gapChar bug in AlignView method
gmungoc [Tue, 1 Sep 2015 15:39:16 +0000 (16:39 +0100)]
JAL-1693 split frame opened for get xrefs, translate as cDNA
Jim Procter [Tue, 1 Sep 2015 15:36:09 +0000 (16:36 +0100)]
JAL-1853 test demonstrating bug
gmungoc [Tue, 1 Sep 2015 12:47:37 +0000 (13:47 +0100)]
JAL-1672 additional assertions added
gmungoc [Tue, 1 Sep 2015 12:47:05 +0000 (13:47 +0100)]
JAL-1355 user error message text externalised
tcofoegbu [Tue, 1 Sep 2015 11:37:59 +0000 (12:37 +0100)]
JAL-1668 house keeping
tcofoegbu [Mon, 31 Aug 2015 17:36:39 +0000 (18:36 +0100)]
merge
tcofoegbu [Mon, 31 Aug 2015 17:35:40 +0000 (18:35 +0100)]
JAL-1700 updated error handling with suggested improvements after Jim's testing
gmungoc [Fri, 28 Aug 2015 15:31:33 +0000 (16:31 +0100)]
JAL-1836 temporary workaround for negative resNumIns in PDB file
gmungoc [Thu, 27 Aug 2015 15:50:06 +0000 (16:50 +0100)]
JAL-1270 comments added regarding required remote service
gmungoc [Thu, 27 Aug 2015 15:49:00 +0000 (16:49 +0100)]
JAL-1759 updated unit test for removal of trim on Atom.resNumIns
gmungoc [Thu, 27 Aug 2015 15:33:19 +0000 (16:33 +0100)]
JAL-1830 tests relocated to AlignViewportTest after refactoring
gmungoc [Thu, 27 Aug 2015 15:31:58 +0000 (16:31 +0100)]
JAL-1627 updated expected tooltip text in unit test
gmungoc [Thu, 27 Aug 2015 15:30:54 +0000 (16:30 +0100)]
JAL-1830 unit tests for removing (or not) mappings on close frame
gmungoc [Thu, 27 Aug 2015 14:26:58 +0000 (15:26 +0100)]
JAL-1830 refactored so no jalview.gui references from jalview.structure
gmungoc [Thu, 27 Aug 2015 14:24:34 +0000 (15:24 +0100)]
JAL-845 compacting duplicated code
gmungoc [Thu, 27 Aug 2015 14:22:17 +0000 (15:22 +0100)]
JAL-1611 debug sysout suppressed
gmungoc [Thu, 27 Aug 2015 13:56:41 +0000 (14:56 +0100)]
JAL-1544 message label corrected
gmungoc [Thu, 27 Aug 2015 11:34:07 +0000 (12:34 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 27 Aug 2015 11:33:55 +0000 (12:33 +0100)]
JAL-1701 help page for Split Frame view linked in
Jim Procter [Thu, 27 Aug 2015 11:23:17 +0000 (12:23 +0100)]
JAL-1844 adding more missing jars - jersey, other json stuff, jsr311 and also jetty (for JAL-1575 JAL-1725)
gmungoc [Thu, 27 Aug 2015 11:00:37 +0000 (12:00 +0100)]
JAL-1544 'Jalview' consistently capitalised
gmungoc [Thu, 27 Aug 2015 10:59:03 +0000 (11:59 +0100)]
JAL-892 JAL-1764 Varna and Chimera also saved to project file
gmungoc [Thu, 27 Aug 2015 10:55:55 +0000 (11:55 +0100)]
JAL-892 saved to project; external help link updated
gmungoc [Thu, 27 Aug 2015 10:53:37 +0000 (11:53 +0100)]
JAL-1727 added EBI mirror of DAS registry
gmungoc [Thu, 27 Aug 2015 10:51:30 +0000 (11:51 +0100)]
JAL-1596 JAL-1725 JAL-1588 updates for selection in Chimera, save to
Project, Windows Firewall
gmungoc [Thu, 27 Aug 2015 10:45:47 +0000 (11:45 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 27 Aug 2015 10:45:36 +0000 (11:45 +0100)]
JAL-1725 restrict Jalview's Jetty server to localhost
Jim Procter [Thu, 27 Aug 2015 10:44:05 +0000 (11:44 +0100)]
fix for JAL-1844 add jersey-core,json,client-1.19 to install anywhere config
gmungoc [Wed, 26 Aug 2015 14:40:12 +0000 (15:40 +0100)]
JAL-1830 dropped reference counts for mappings, instead remove mapping
when no alignment holds a reference to it
gmungoc [Wed, 26 Aug 2015 14:30:50 +0000 (15:30 +0100)]
JAL-1596 check for null pointer (thread running after viewer closed)
gmungoc [Wed, 26 Aug 2015 14:26:46 +0000 (15:26 +0100)]
JAL-1270 test separated out of JalviewChimeraView
gmungoc [Wed, 26 Aug 2015 14:25:54 +0000 (15:25 +0100)]
JAL-1270 corrected path to test properties file
gmungoc [Wed, 26 Aug 2015 14:25:21 +0000 (15:25 +0100)]
JAL-1270 separated Jmol and Chimera tests to avoid concurrency problems
gmungoc [Wed, 26 Aug 2015 13:51:52 +0000 (14:51 +0100)]
JAL-1759 updated unit test for removal of trim of Atom.resNumIns
gmungoc [Wed, 26 Aug 2015 11:06:35 +0000 (12:06 +0100)]
JAL-1840 correct setting status bar for structure mouseover
gmungoc [Wed, 26 Aug 2015 11:03:45 +0000 (12:03 +0100)]
JAL-1759 added check for null (console 'history')
gmungoc [Wed, 26 Aug 2015 11:01:03 +0000 (12:01 +0100)]
Fix to use correct resource bundle entry
gmungoc [Wed, 26 Aug 2015 10:59:35 +0000 (11:59 +0100)]
JAL-1759 corrected syntax for 'atom picked' callback (toggles label
on/off in Jmol)
gmungoc [Tue, 25 Aug 2015 09:50:52 +0000 (10:50 +0100)]
JAL-1780 just a spelling change
gmungoc [Tue, 25 Aug 2015 09:42:45 +0000 (10:42 +0100)]
JAL-1674 more correct status bars in splitframe mouseover (applet)
gmungoc [Mon, 24 Aug 2015 12:05:32 +0000 (13:05 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 24 Aug 2015 12:05:09 +0000 (13:05 +0100)]
JAL-1759 removed trim() of Atom.resNumIns as not backwards compatible
with saved projects (generates duplicate annotations)
tcofoegbu [Mon, 24 Aug 2015 10:13:20 +0000 (11:13 +0100)]
JAL-1641 externalised save_as_biojs_html
tcofoegbu [Mon, 24 Aug 2015 10:06:31 +0000 (11:06 +0100)]
JAL-1835 corrected Embbed to Embed
tcofoegbu [Mon, 24 Aug 2015 08:39:26 +0000 (09:39 +0100)]
merge
tcofoegbu [Mon, 24 Aug 2015 08:36:56 +0000 (09:36 +0100)]
JAL-1834 removed quotes around truncated strings with ellipsis
gmungoc [Mon, 24 Aug 2015 08:25:22 +0000 (09:25 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 24 Aug 2015 08:25:01 +0000 (09:25 +0100)]
JAL-845 error message on syserr if supplied files don't map as cDNA and
protein
gmungoc [Mon, 24 Aug 2015 08:16:46 +0000 (09:16 +0100)]
remove mentions of non-functional RNAInteraction colourscheme
tcofoegbu [Fri, 21 Aug 2015 16:05:14 +0000 (17:05 +0100)]
JAL-1834 capped the tool-tip text at 500. once that is exceeded an ellipsis is added
tcofoegbu [Fri, 21 Aug 2015 13:59:19 +0000 (14:59 +0100)]
JAL-1834 disabled action buttons (Back / Ok / Cancel) when in 'Configure Displayed Columns' tab
tcofoegbu [Fri, 21 Aug 2015 10:27:19 +0000 (11:27 +0100)]
JAL-1443 bug fix for loading pasted alignments from clipboard via the file loader
tcofoegbu [Fri, 21 Aug 2015 09:50:35 +0000 (10:50 +0100)]
JAL-1831 updated json schema doc
tcofoegbu [Fri, 21 Aug 2015 09:47:43 +0000 (10:47 +0100)]
clean up
tcofoegbu [Fri, 21 Aug 2015 09:43:10 +0000 (10:43 +0100)]
JAL-1780 made the 'Select All' checkbox to be shown for all the setting panels
tcofoegbu [Fri, 21 Aug 2015 09:18:15 +0000 (10:18 +0100)]
JAL-1780 changed 'Check All' to 'Select All' and externalised all message labels in export settings window
tcofoegbu [Thu, 20 Aug 2015 14:00:13 +0000 (15:00 +0100)]
merge
tcofoegbu [Thu, 20 Aug 2015 12:58:10 +0000 (13:58 +0100)]
JAL-1833 revised implementation
gmungoc [Thu, 20 Aug 2015 08:42:44 +0000 (09:42 +0100)]
JAL-1833 added unit tests (some failing) for wrapToolitp
gmungoc [Wed, 19 Aug 2015 09:00:40 +0000 (10:00 +0100)]
JAL-1782 don't save TESTNG output summary to git
gmungoc [Wed, 19 Aug 2015 08:40:27 +0000 (09:40 +0100)]
JAL-1725 log to sysout when listener shuts down
gmungoc [Wed, 19 Aug 2015 08:39:26 +0000 (09:39 +0100)]
JAL-1742 suppress 'add chain' option for Jmol, pull up shared code for
Jmol/Chimera
tcofoegbu [Tue, 18 Aug 2015 15:17:28 +0000 (16:17 +0100)]
JAL-1861 bugfix to allow parsing of stockholm files with missing annotations
tcofoegbu [Tue, 18 Aug 2015 13:24:32 +0000 (14:24 +0100)]
JAL-1835 added UI for BioJSON embbeding preference
tcofoegbu [Tue, 18 Aug 2015 12:22:36 +0000 (13:22 +0100)]
JAL-1835 made BioJSON embedding to html exports configurable, and trapped import of html files without BioJSON
tcofoegbu [Tue, 18 Aug 2015 10:47:46 +0000 (11:47 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 18 Aug 2015 10:47:32 +0000 (11:47 +0100)]
JAL-1834 added tooltip to the PDB sequence fetcher and structure chooser summary tables
git://source.jalview.org / jalview.git / log