Jim Procter [Thu, 23 Jul 2015 10:27:57 +0000 (11:27 +0100)]
JAL-1819 commented out debugging message to stderr
Jim Procter [Thu, 23 Jul 2015 10:27:15 +0000 (11:27 +0100)]
JAL-1551 JAL-1819 formatting/imports
Jim Procter [Thu, 23 Jul 2015 10:26:11 +0000 (11:26 +0100)]
JAL-1819 use Float.isNaN() to check for NaNs!
gmungoc [Wed, 8 Jul 2015 12:19:14 +0000 (13:19 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 8 Jul 2015 12:18:49 +0000 (13:18 +0100)]
JAL-1598 replaced faulty regex, amended Varna call, to get pseudo-knots
tcofoegbu [Wed, 8 Jul 2015 11:10:05 +0000 (12:10 +0100)]
JAL-1641 biojson documentation with docson
tcofoegbu [Tue, 7 Jul 2015 15:18:41 +0000 (16:18 +0100)]
JAL-1769 fixed output to jalview (.jpv) file in headless mode. Initial cause of failure: NPE while trying to save varna viewers (Desktop.destop is null in headless mode)
tcofoegbu [Tue, 7 Jul 2015 14:40:54 +0000 (15:40 +0100)]
JAL-1805 test envirionment separation
tcofoegbu [Mon, 6 Jul 2015 16:01:28 +0000 (17:01 +0100)]
Merge branch 'features/1769_headless-mode-test' into develop
tcofoegbu [Mon, 6 Jul 2015 16:00:25 +0000 (17:00 +0100)]
JAL-1641 added json schema for jalview JSON model, the schema is employed for documentation but can be more usefull for validation in the future
tcofoegbu [Mon, 6 Jul 2015 15:58:20 +0000 (16:58 +0100)]
JAL-1769 fixed headless execution mode and created test for all possible outputs
gmungoc [Mon, 6 Jul 2015 15:23:21 +0000 (16:23 +0100)]
JAL-1081 unit tests added
gmungoc [Mon, 6 Jul 2015 11:03:19 +0000 (12:03 +0100)]
JAL-1782 refactored test to ensure it passes in TestNG
gmungoc [Mon, 6 Jul 2015 11:02:33 +0000 (12:02 +0100)]
JAL-1421 generics used for leaner safer code
gmungoc [Mon, 6 Jul 2015 09:20:56 +0000 (10:20 +0100)]
JAL-1799 tweaked calculation for applet, now showing 2 not 3 seqs
gmungoc [Mon, 6 Jul 2015 08:01:52 +0000 (09:01 +0100)]
JAL-1799 equivalent logic in applet
gmungoc [Fri, 3 Jul 2015 10:33:11 +0000 (11:33 +0100)]
JAL-892 jnlp, installAnywhere, build, licence references updated to 3.93
gmungoc [Fri, 3 Jul 2015 10:18:22 +0000 (11:18 +0100)]
Merge branch 'develop' into features/JAL-892varnaToProject
gmungoc [Fri, 3 Jul 2015 10:07:23 +0000 (11:07 +0100)]
JAL-892 1 second delay for correct initial rendering; code tidy up
tcofoegbu [Thu, 2 Jul 2015 15:38:40 +0000 (16:38 +0100)]
Merge branch 'bug/JAL-1443_loading-empty-file' into develop
tcofoegbu [Thu, 2 Jul 2015 15:37:56 +0000 (16:37 +0100)]
JAL-1443 data validation for empty content before loading alignment from file or clipboard
gmungoc [Thu, 2 Jul 2015 14:27:03 +0000 (15:27 +0100)]
JAL-1677 check all response lines when parsing REST server port
gmungoc [Wed, 1 Jul 2015 14:53:40 +0000 (15:53 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 1 Jul 2015 14:53:27 +0000 (15:53 +0100)]
JAL-1681 more condensed tooltip where codons share same percentage
tcofoegbu [Wed, 1 Jul 2015 14:23:19 +0000 (15:23 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 1 Jul 2015 14:23:11 +0000 (15:23 +0100)]
house keeping
gmungoc [Wed, 1 Jul 2015 13:29:16 +0000 (14:29 +0100)]
JAL-1802 explanatory comment added
gmungoc [Wed, 1 Jul 2015 13:15:19 +0000 (14:15 +0100)]
JAL-1802 handle slide sequences edits in split frame mode
gmungoc [Wed, 1 Jul 2015 10:48:04 +0000 (11:48 +0100)]
JAL-1799 deduct more space for decorators on Windows
gmungoc [Wed, 1 Jul 2015 08:13:22 +0000 (09:13 +0100)]
JAL-1619 align the added sequences to match what they are added to
tcofoegbu [Tue, 30 Jun 2015 11:42:25 +0000 (12:42 +0100)]
Merge branch 'features/JAL-1641_JSON-tests-and-docs' into develop
tcofoegbu [Tue, 30 Jun 2015 11:40:21 +0000 (12:40 +0100)]
JAL-1641 round trip test/refactoring
gmungoc [Tue, 30 Jun 2015 11:14:45 +0000 (12:14 +0100)]
JAL-1691 trackpad scrolling goes to full width even with short sequences
gmungoc [Mon, 29 Jun 2015 15:31:40 +0000 (16:31 +0100)]
JAL-1799 adjusted annotation height calculation
tcofoegbu [Fri, 26 Jun 2015 16:06:05 +0000 (17:06 +0100)]
JAL-1641 fixed broken functionalities after refactor
gmungoc [Fri, 26 Jun 2015 15:59:39 +0000 (16:59 +0100)]
JAL-1782 BeforeMethod added to fix test in NG
gmungoc [Fri, 26 Jun 2015 14:50:57 +0000 (15:50 +0100)]
Merge branch 'develop' into features/JAL-892varnaToProject
tcofoegbu [Fri, 26 Jun 2015 09:42:27 +0000 (10:42 +0100)]
merge
tcofoegbu [Fri, 26 Jun 2015 09:41:32 +0000 (10:41 +0100)]
JAL-1780 improvement to ensure export settings dialog is not invoked if there's noting to configure and clean ups
Jim Procter [Thu, 25 Jun 2015 10:13:09 +0000 (11:13 +0100)]
JAL-1691 avoid NPE when original split frame has been closed before the alignment completes. See JAL-1792 for enhancement on this code.
Jim Procter [Thu, 25 Jun 2015 10:06:45 +0000 (11:06 +0100)]
JAL-1780 JAL-653 JAL-1892 brackets in wrong place broke ‘add to file’ for splitframe/cdna/protein
also formatted file for clarity
Jim Procter [Wed, 24 Jun 2015 20:51:35 +0000 (21:51 +0100)]
Merge branch 'features/JAL-1370_patchshowunconserved' into develop
Jim Procter [Wed, 24 Jun 2015 15:36:48 +0000 (16:36 +0100)]
JAL-1790 fix: javac.source=1.7 and javac.target=1.7 variables for all javac tasks in build.xml
Jim Procter [Wed, 24 Jun 2015 15:18:12 +0000 (16:18 +0100)]
JAL-653 JAL-1780 JAL-1892 fix jalviewLite compilation
Jim Procter [Wed, 24 Jun 2015 14:11:45 +0000 (15:11 +0100)]
Merge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892' into develop
Jim Procter [Tue, 23 Jun 2015 12:26:11 +0000 (13:26 +0100)]
JAL-1780 JAL-653 jim forgot to put the conditional action in!
Jim Procter [Tue, 23 Jun 2015 08:48:13 +0000 (09:48 +0100)]
JAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refactored test suite with TestNG
Jim Procter [Mon, 22 Jun 2015 18:43:33 +0000 (19:43 +0100)]
JAL-1270 fix logic in stockholm test allowing annotation.description to be equivalent if both are null, or one or both is an empty string, or a whitespace string
Jim Procter [Mon, 22 Jun 2015 18:21:59 +0000 (19:21 +0100)]
JAL-653 JAL-1780 JAL-1140 added RNAML example alignment file
Jim Procter [Mon, 22 Jun 2015 18:21:07 +0000 (19:21 +0100)]
JAL-653 JAL-1780 dropped unnecessary refs
Jim Procter [Mon, 22 Jun 2015 18:12:07 +0000 (19:12 +0100)]
JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses AlignmentI where possible, and allows configuration via Alignment Panel and ExportSettings interface references
Jim Procter [Mon, 22 Jun 2015 17:26:23 +0000 (18:26 +0100)]
JAL-653 JAL-1780 reorder imports
gmungoc [Mon, 22 Jun 2015 13:05:12 +0000 (14:05 +0100)]
JAL-892 tidy Varna panel names; JAL-1789 simplified mouseover
gmungoc [Mon, 22 Jun 2015 12:34:58 +0000 (13:34 +0100)]
JAL-893 upgrade to VARNAv3-93.jar
Jim Procter [Fri, 19 Jun 2015 16:45:50 +0000 (17:45 +0100)]
JAL-653 JAL-1780 refactor getGroups so HTMLfile/JSONfile adopt same pattern as other parsers
Jim Procter [Fri, 19 Jun 2015 16:44:27 +0000 (17:44 +0100)]
JAL-1780 JAL-653 organise imports
gmungoc [Fri, 19 Jun 2015 16:11:17 +0000 (17:11 +0100)]
JAL-892 check viewer is linked to alignment panel on save to XML
Jim Procter [Fri, 19 Jun 2015 15:14:39 +0000 (16:14 +0100)]
JAL-653 JAL-1780 minimise call rate now av.hasHiddenRows is dynamic
Jim Procter [Fri, 19 Jun 2015 15:13:48 +0000 (16:13 +0100)]
JAL-653 JAL-1780 dropped av.setHasHiddenRows() and made av.hasHiddenRows() dynamic rather than a maintained flag
tcofoegbu [Fri, 19 Jun 2015 15:04:33 +0000 (16:04 +0100)]
JAL-1270 test suits import order refactor
Jim Procter [Fri, 19 Jun 2015 15:02:05 +0000 (16:02 +0100)]
JAL-1780 JAL-653 organise imports
tcofoegbu [Fri, 19 Jun 2015 13:04:02 +0000 (14:04 +0100)]
JAL-1270 JUnit to TestNG refactoring
Jim Procter [Thu, 18 Jun 2015 18:07:17 +0000 (19:07 +0100)]
JAL-653 patch broken test code - test still not passing
Jim Procter [Thu, 18 Jun 2015 18:06:56 +0000 (19:06 +0100)]
JAL-653 JAL-1780 JAL-1543 javadoc and comment about further refactoring
Jim Procter [Thu, 18 Jun 2015 18:00:05 +0000 (19:00 +0100)]
JAL-653 JAL-1780 javadoc for FeatureRenderer prior to splitting into model and renderer concerns
Jim Procter [Thu, 18 Jun 2015 17:54:53 +0000 (18:54 +0100)]
JAL-1780 JAL-653 moved AlignExportSettings reference on AlignViewportI to FileParse, use AlignmentViewPanel for getting FeatureRender
gmungoc [Thu, 18 Jun 2015 16:15:23 +0000 (17:15 +0100)]
JAL-1270 test added
gmungoc [Thu, 18 Jun 2015 16:14:38 +0000 (17:14 +0100)]
JAL-1544 typos in comments
gmungoc [Thu, 18 Jun 2015 16:13:10 +0000 (17:13 +0100)]
JAL-892 JAL-1779 save/restore Varna viewer to/from project
gmungoc [Thu, 18 Jun 2015 16:09:32 +0000 (17:09 +0100)]
JAL-1695 default ENABLE_SPLIT_FRAME to true for desktop
(enableSplitFrame false for applet)
gmungoc [Thu, 18 Jun 2015 16:05:17 +0000 (17:05 +0100)]
JAL-892 schema changes (rnaViewer) for save Varna to project
gmungoc [Thu, 18 Jun 2015 08:18:14 +0000 (09:18 +0100)]
JAL-1781 annotation.sequenceRef now sequence id not name, incrementing
annotation ids
Jim Procter [Wed, 17 Jun 2015 20:54:39 +0000 (21:54 +0100)]
JAL-1784 minimise data duplication, and report out of memory errors and other kinds of parsing problems to the user
Jim Procter [Wed, 17 Jun 2015 20:50:15 +0000 (21:50 +0100)]
JAL-1784 refactor parse method to directly parse FileParser input reader stream.
Jim Procter [Wed, 17 Jun 2015 15:42:09 +0000 (16:42 +0100)]
Merge branch 'features/JAL-653_gffalignments' into trial/JAL-1780_JAL-653
Jim Procter [Wed, 17 Jun 2015 15:35:29 +0000 (16:35 +0100)]
Merge branch 'develop' into features/JAL-653_gffalignments
update for incoming changes and finessing against JAL-1641
Jim Procter [Wed, 17 Jun 2015 14:58:48 +0000 (15:58 +0100)]
Merge branch 'develop' into features/JAL-1780_export-settings_flatfile
Jim Procter [Wed, 17 Jun 2015 14:53:41 +0000 (15:53 +0100)]
JAL-1783 add java 1.7 and 1.8 class numbers
Jim Procter [Wed, 17 Jun 2015 10:40:07 +0000 (11:40 +0100)]
Merge branch 'develop' into features/JAL-1780_export-settings_flatfile
tcofoegbu [Wed, 17 Jun 2015 10:22:22 +0000 (11:22 +0100)]
JAL-1780 more support for export setting for flatfile output
tcofoegbu [Wed, 17 Jun 2015 10:16:58 +0000 (11:16 +0100)]
JAL-1780 Export settings for flatfile output
gmungoc [Wed, 17 Jun 2015 08:30:03 +0000 (09:30 +0100)]
JAL-1588 restore ChimeraViewFrame geometry as well
gmungoc [Wed, 17 Jun 2015 07:50:13 +0000 (08:50 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 17 Jun 2015 07:49:34 +0000 (08:49 +0100)]
JAL-1778 reinstated this.ssm to handle 'close all windows' robustly
Jim Procter [Mon, 15 Jun 2015 17:58:55 +0000 (18:58 +0100)]
Merge branch 'bug/JAL-1775' into develop
Jim Procter [Mon, 15 Jun 2015 17:52:02 +0000 (18:52 +0100)]
JAL-1665 patch for regression: failing jalview.ws.jabaws.DisorderAnnotExportImport due to different sequence features in original and reimported alignment (originally, sequence features were not available on local sequenceI)
Jim Procter [Mon, 15 Jun 2015 17:39:28 +0000 (18:39 +0100)]
JAL-1775 patch for regression from Anne Menard’s pseudo knot support JAL-1598
Jim Procter [Mon, 15 Jun 2015 16:07:45 +0000 (17:07 +0100)]
Merge branch 'bug/JAL-1775' into develop
Jim Procter [Mon, 15 Jun 2015 16:06:51 +0000 (17:06 +0100)]
JAL-1775 patch regression bug when displayChar is null and secondaryStructure contains secondary structure info
Jim Procter [Mon, 15 Jun 2015 15:09:37 +0000 (16:09 +0100)]
Merge branch 'bug/JAL-1775' into develop
Jim Procter [Mon, 15 Jun 2015 15:08:47 +0000 (16:08 +0100)]
fix for JAL-1775 (and reorganise imports)
Jim Procter [Mon, 15 Jun 2015 14:24:38 +0000 (15:24 +0100)]
Merge branch 'bug/JAL-1775' into develop
Jim Procter [Mon, 15 Jun 2015 13:03:22 +0000 (14:03 +0100)]
JAL-1775 test demonstrating bug
Jim Procter [Mon, 15 Jun 2015 13:03:07 +0000 (14:03 +0100)]
JAL-1775 FileLoader javadoc
Jim Procter [Mon, 15 Jun 2015 13:02:37 +0000 (14:02 +0100)]
Jim Procter [Mon, 15 Jun 2015 12:37:44 +0000 (13:37 +0100)]
Merge branch 'develop' into bug/JAL-1775
gmungoc [Mon, 15 Jun 2015 11:19:54 +0000 (12:19 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 15 Jun 2015 11:18:55 +0000 (12:18 +0100)]
JAL-1778 deregister as a listener when panel closed
Jim Procter [Mon, 15 Jun 2015 10:42:52 +0000 (11:42 +0100)]
JAL-1775 fix broken test due to missing file (RF0031_unfolded).
tcofoegbu [Mon, 15 Jun 2015 10:39:23 +0000 (11:39 +0100)]
JAL-1641 clean up
git://source.jalview.org / jalview.git / log