gmungoc [Thu, 16 Nov 2017 09:05:03 +0000 (09:05 +0000)]
JAL-2835 update test for array-valued attribute name
gmungoc [Thu, 16 Nov 2017 09:03:49 +0000 (09:03 +0000)]
JAL-2835 update test for CSQ data held as a Map
gmungoc [Thu, 16 Nov 2017 08:18:10 +0000 (08:18 +0000)]
JAL-2835 test updated for colour by 'nested attribute'
gmungoc [Thu, 16 Nov 2017 08:13:52 +0000 (08:13 +0000)]
JAL-2816 tests for findFeaturesAtColumn
kiramt [Wed, 15 Nov 2017 16:22:21 +0000 (16:22 +0000)]
JAL-2831 Don't show cursor if position in hidden region
kiramt [Wed, 15 Nov 2017 16:05:18 +0000 (16:05 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
gmungoc [Wed, 15 Nov 2017 15:47:41 +0000 (15:47 +0000)]
JAL-2816 exclude filtered / thresholded out features when finding
kiramt [Wed, 15 Nov 2017 13:23:00 +0000 (13:23 +0000)]
JAL-2811 Updated following review
kiramt [Wed, 15 Nov 2017 11:44:44 +0000 (11:44 +0000)]
JAL-2840 fix wrapped scrolling when using cursor at a hidden region
kiramt [Wed, 15 Nov 2017 11:17:41 +0000 (11:17 +0000)]
JAL-2834 JAL-2836 temporarily disabled wrapped mode fastpaint
gmungoc [Wed, 15 Nov 2017 10:51:51 +0000 (10:51 +0000)]
JAL-2835 spike updated with latest
gmungoc [Wed, 15 Nov 2017 10:50:19 +0000 (10:50 +0000)]
JAL-2835 take all CSQ fields; catch invalid field match patterns
gmungoc [Wed, 15 Nov 2017 10:42:49 +0000 (10:42 +0000)]
JAL-2835 support filter/colour by nested attribute names
gmungoc [Wed, 15 Nov 2017 10:41:45 +0000 (10:41 +0000)]
JAL-2835 code tidy (generic type constructors)
gmungoc [Wed, 15 Nov 2017 10:38:21 +0000 (10:38 +0000)]
JAL-2069 dialog title now 'Variable colour'
gmungoc [Wed, 15 Nov 2017 10:36:23 +0000 (10:36 +0000)]
JAL- 2835 support filter on nested attribute keys
gmungoc [Wed, 15 Nov 2017 10:34:28 +0000 (10:34 +0000)]
JAL-2835 add filters for VCF/VEP 'fields of interest'
gmungoc [Wed, 15 Nov 2017 10:32:41 +0000 (10:32 +0000)]
JAL-1270 add missing "Functional" to tests
kiramt [Wed, 15 Nov 2017 08:47:47 +0000 (08:47 +0000)]
JAL-2831 ported to applet
kiramt [Tue, 14 Nov 2017 19:36:53 +0000 (19:36 +0000)]
JAL-2831 tidies and tests
kiramt [Tue, 14 Nov 2017 16:03:47 +0000 (16:03 +0000)]
JAL-2831 tidy
kiramt [Tue, 14 Nov 2017 14:59:52 +0000 (14:59 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Tue, 14 Nov 2017 14:56:37 +0000 (14:56 +0000)]
JAL-2811 Changed to overlay on via graphics context, not separate image
kiramt [Tue, 14 Nov 2017 14:10:30 +0000 (14:10 +0000)]
JAL-2811 Missed commit
kiramt [Tue, 14 Nov 2017 13:43:40 +0000 (13:43 +0000)]
JAL-2811 Made it work for hidden columns/seqs too
kiramt [Tue, 14 Nov 2017 12:11:21 +0000 (12:11 +0000)]
JAL-2831 Attempt at cursor fix for wrapped mode
Jim Procter [Tue, 14 Nov 2017 12:11:04 +0000 (12:11 +0000)]
JAL-2758 update uniprot retrieval test
kiramt [Tue, 14 Nov 2017 11:12:55 +0000 (11:12 +0000)]
Merge branch 'bug/JAL-2811' into bug/JAL-2831
kiramt [Tue, 14 Nov 2017 10:33:33 +0000 (10:33 +0000)]
JAL-2831 deal with hidden cols and seqs in new cursor code
kiramt [Tue, 14 Nov 2017 10:15:46 +0000 (10:15 +0000)]
JAL-2831 Added move viewport event and set up cursor code to use it
kiramt [Tue, 14 Nov 2017 09:30:31 +0000 (09:30 +0000)]
Merge branch 'imp/JAL-2774' into bug/JAL-2831
gmungoc [Tue, 14 Nov 2017 08:44:08 +0000 (08:44 +0000)]
JAL-2754 corrected merge conflict
Jim Procter [Mon, 13 Nov 2017 20:25:06 +0000 (20:25 +0000)]
JAL-2758 release notes
Jim Procter [Mon, 13 Nov 2017 20:22:01 +0000 (20:22 +0000)]
JAL-2698 formatting
kiramt [Mon, 13 Nov 2017 19:40:06 +0000 (19:40 +0000)]
JAL-2811 Tidy
Jim Procter [Mon, 13 Nov 2017 18:59:59 +0000 (18:59 +0000)]
Merge branch 'features/JAL-2758_shorteruniprot' into develop
Jim Procter [Mon, 13 Nov 2017 18:57:10 +0000 (18:57 +0000)]
JAL-2758 remove configurable behaviour - Uniprot sequences are only assigned IDs derived from Entry name
Jim Procter [Mon, 13 Nov 2017 18:56:22 +0000 (18:56 +0000)]
JAL-2758 typo
gmungoc [Mon, 13 Nov 2017 16:57:02 +0000 (16:57 +0000)]
JAL-2738 stubs for filtering VEP and VCF fields of interest
kiramt [Mon, 13 Nov 2017 16:42:20 +0000 (16:42 +0000)]
JAl-2811 Working for wrapped panels too
gmungoc [Mon, 13 Nov 2017 16:39:02 +0000 (16:39 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
Conflicts:
.classpath
build.xml
resources/lang/Messages.properties
gmungoc [Mon, 13 Nov 2017 16:23:12 +0000 (16:23 +0000)]
JAL-2662 tweak README, format code
Jim Procter [Mon, 13 Nov 2017 16:05:37 +0000 (16:05 +0000)]
JAL-2698 what's new...
kiramt [Mon, 13 Nov 2017 15:53:12 +0000 (15:53 +0000)]
JAL-2811 Add layer for cursor in SeqCanvas
Jim Procter [Mon, 13 Nov 2017 15:41:10 +0000 (15:41 +0000)]
JAL-2810 release notes
Jim Procter [Mon, 13 Nov 2017 15:38:34 +0000 (15:38 +0000)]
Merge branch 'imp/JAL-2810_ftsIDtab' into develop
Jim Procter [Mon, 13 Nov 2017 15:32:05 +0000 (15:32 +0000)]
JAL-2698 stub for 2.10.3 new known issues entries
Jim Procter [Mon, 13 Nov 2017 15:31:05 +0000 (15:31 +0000)]
JAL-2702 groovy interpreter update and java 9 jnlp release notes
Jim Procter [Mon, 13 Nov 2017 15:03:27 +0000 (15:03 +0000)]
Merge branch 'bug/JAL-2702_groovyconsoleJava9' into develop
Jim Procter [Mon, 13 Nov 2017 14:33:06 +0000 (14:33 +0000)]
JAL-2702 --illegal-access=warn for JVM launch
gmungoc [Mon, 13 Nov 2017 14:11:08 +0000 (14:11 +0000)]
JAL-2176 removed unused Sequence.index
Jim Procter [Mon, 13 Nov 2017 13:52:48 +0000 (13:52 +0000)]
JAL-2702 update to groovy 2.4.12
Jim Procter [Mon, 13 Nov 2017 13:00:17 +0000 (13:00 +0000)]
JAL-2810 updated help docs for auto search checkbox and retrieve IDs tab
kiramt [Mon, 13 Nov 2017 12:46:37 +0000 (12:46 +0000)]
JAL-2784 new checks for gg==null
Jim Procter [Mon, 13 Nov 2017 12:44:08 +0000 (12:44 +0000)]
JAL-2810 updated screenshots in documentation
Jim Procter [Mon, 13 Nov 2017 12:43:38 +0000 (12:43 +0000)]
JAL-2810 auto search checkbox state stored as user preference. Enabled by default.
gmungoc [Mon, 13 Nov 2017 12:02:43 +0000 (12:02 +0000)]
JAL-2679 example accession changed to
CAD01290
Jim Procter [Mon, 13 Nov 2017 11:53:27 +0000 (11:53 +0000)]
JAL-2810 mainFramTabs -> tabs
Jim Procter [Mon, 13 Nov 2017 11:53:02 +0000 (11:53 +0000)]
JAL-2810 simpler tooltip (assume user will work out that pressing return will update results)
Jim Procter [Fri, 10 Nov 2017 16:46:15 +0000 (16:46 +0000)]
JAL-2828 allow CalcId to match on String equivalence (migrated from Alignment’s implementation of findAnnotation)
Jim Procter [Fri, 10 Nov 2017 16:37:35 +0000 (16:37 +0000)]
JAL-2828 refactored duplicate code for searching lists of AlignmentAnnotation to static methods.
gmungoc [Fri, 10 Nov 2017 15:56:11 +0000 (15:56 +0000)]
JAL-2829 fixes and unit tests
gmungoc [Fri, 10 Nov 2017 15:38:19 +0000 (15:38 +0000)]
JAL-2562 updated findPosition javadoc to match behaviour
gmungoc [Fri, 10 Nov 2017 15:10:50 +0000 (15:10 +0000)]
JAL-2829 unit tests for failing cases
kiramt [Fri, 10 Nov 2017 10:08:50 +0000 (10:08 +0000)]
JAL-2827 related fixes for stem and non-canonical annotation
gmungoc [Fri, 10 Nov 2017 09:05:18 +0000 (09:05 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
kiramt [Thu, 9 Nov 2017 20:05:31 +0000 (20:05 +0000)]
JAL-2827 Fix notched repaint of helix annotation when scrolling
Jim Procter [Wed, 8 Nov 2017 17:02:42 +0000 (17:02 +0000)]
Merge branch 'bug/JAL-2742' into develop
Jim Procter [Wed, 8 Nov 2017 17:02:06 +0000 (17:02 +0000)]
Revert "JAL-2742 release notes - pending confirmation that there was impact to user"
-- no impact so won't include development detail in release notes.
This reverts commit
ba70dbddc08876d8d72bb303823f683b65bf13c7.
Jim Procter [Wed, 8 Nov 2017 16:57:14 +0000 (16:57 +0000)]
JAL-2225 release note
Jim Procter [Wed, 8 Nov 2017 16:52:03 +0000 (16:52 +0000)]
Merge branch 'bug/JAL-2225mapMultipleChains' into develop
gmungoc [Wed, 8 Nov 2017 15:46:56 +0000 (15:46 +0000)]
JAL-2808 i18n, widget state settings
Jim Procter [Wed, 8 Nov 2017 15:21:13 +0000 (15:21 +0000)]
Merge branch 'develop' into bug/JAL-2225mapMultipleChains
gmungoc [Wed, 8 Nov 2017 11:34:40 +0000 (11:34 +0000)]
JAL-2069 updated spike to latest
gmungoc [Wed, 8 Nov 2017 11:33:43 +0000 (11:33 +0000)]
JAL-2069 ensure threshline instantiated to avoid NPE
gmungoc [Wed, 8 Nov 2017 11:13:41 +0000 (11:13 +0000)]
JAL-2069 (helper method for) italic titled borders
Jim Procter [Tue, 7 Nov 2017 17:33:07 +0000 (17:33 +0000)]
JAL-2698 14 Nov 2017 release date for 2.10.3
Jim Procter [Tue, 7 Nov 2017 17:27:46 +0000 (17:27 +0000)]
JAL-2775 release notes
Jim Procter [Tue, 7 Nov 2017 17:25:51 +0000 (17:25 +0000)]
Merge branch 'imp/JAL-2775' into develop
Jim Procter [Tue, 7 Nov 2017 17:18:12 +0000 (17:18 +0000)]
JAL-2810 i18n tab label
kiramt [Tue, 7 Nov 2017 17:13:20 +0000 (17:13 +0000)]
JAL-2774 Added javadoc for new event parameters
Jim Procter [Tue, 7 Nov 2017 17:12:45 +0000 (17:12 +0000)]
JAL-2810 ‘Close’ is now ‘Cancel’ in SequenceFetcher panel
Jim Procter [Tue, 7 Nov 2017 17:12:08 +0000 (17:12 +0000)]
JAL-2810 working back button shown for bulk ID retrieval tab in FTS search
kiramt [Tue, 7 Nov 2017 17:09:30 +0000 (17:09 +0000)]
JAL-2774 Fix fastpaint of wrapped alignment
kiramt [Tue, 7 Nov 2017 17:02:31 +0000 (17:02 +0000)]
JAL-2821 refactored drawPartialGroupOutline
gmungoc [Tue, 7 Nov 2017 16:40:57 +0000 (16:40 +0000)]
JAL-2069 update spike to latest (no value colour options)
gmungoc [Tue, 7 Nov 2017 16:40:05 +0000 (16:40 +0000)]
JAL-2069 choice of no / min / max colour if 'no attribute value'
Jim Procter [Tue, 7 Nov 2017 16:37:34 +0000 (16:37 +0000)]
JAL-2810 bulk fetch for PDB IDs
Jim Procter [Tue, 7 Nov 2017 16:30:26 +0000 (16:30 +0000)]
JAL-2804 clearer tooltip for autosearch checkbox
gmungoc [Tue, 7 Nov 2017 13:14:45 +0000 (13:14 +0000)]
JAL-2069 update spike with latest
gmungoc [Tue, 7 Nov 2017 13:13:46 +0000 (13:13 +0000)]
JAL-2069 corrected overloaded constructor behaviour
gmungoc [Tue, 7 Nov 2017 11:50:54 +0000 (11:50 +0000)]
JAL-2069 update spike branch with latest
gmungoc [Tue, 7 Nov 2017 11:49:44 +0000 (11:49 +0000)]
Merge branch 'develop' into features/JAL-1793VCF
gmungoc [Tue, 7 Nov 2017 11:48:16 +0000 (11:48 +0000)]
JAL-2069 add 'by attribute' options to graduated feature colour
gmungoc [Tue, 7 Nov 2017 11:45:49 +0000 (11:45 +0000)]
JAL-2069 add attributeName and noValueColour to FeatureColour
gmungoc [Tue, 7 Nov 2017 11:44:50 +0000 (11:44 +0000)]
JAL-2816 tweaks to feature visibility checks
gmungoc [Tue, 7 Nov 2017 11:16:37 +0000 (11:16 +0000)]
JAL-2808 tweak to use Iterable for set of matchers
gmungoc [Tue, 7 Nov 2017 09:07:03 +0000 (09:07 +0000)]
JAL-2069 JAL-2808 utility method to build combobox with tooltips
gmungoc [Tue, 7 Nov 2017 09:01:44 +0000 (09:01 +0000)]
JAL-2820 limit length of residue tooltip
gmungoc [Mon, 6 Nov 2017 16:44:43 +0000 (16:44 +0000)]
JAL-2069 cache colours generated from labels
git://source.jalview.org / jalview.git / log