gmungoc [Thu, 8 Nov 2018 15:34:57 +0000 (15:34 +0000)]
JAL-1889 ignore Clover instrumentation in test (second attempt)
gmungoc [Thu, 8 Nov 2018 15:24:06 +0000 (15:24 +0000)]
JAL-1889 unit test tweaks for running on server
Ben Soares [Thu, 8 Nov 2018 14:46:17 +0000 (14:46 +0000)]
JAL-1988 tidying, plus don't add Preferences to Tools menu on a Mac\!
Ben Soares [Thu, 8 Nov 2018 14:28:10 +0000 (14:28 +0000)]
JAL-1988 JAVA 11 enabled version with Quit, Preferences and About handlers enabled for Mac. Run with openjdk-11 and 'java -classpath "classes:lib/*:j11lib/*" jalview.bin.Jalview'
Ben Soares [Mon, 5 Nov 2018 16:47:41 +0000 (16:47 +0000)]
JAL-1988 Investigating...
Ben Soares [Mon, 5 Nov 2018 10:01:18 +0000 (10:01 +0000)]
JAL-3141 Slightly improved message and more thorough tests
Ben Soares [Mon, 5 Nov 2018 08:57:38 +0000 (08:57 +0000)]
JAL-3141 couple of minor fixes for example files being displayed in the Preferences tab
Ben Soares [Fri, 2 Nov 2018 16:37:33 +0000 (16:37 +0000)]
JAL-3141 Tests now available and working, bringing to light a problem with the classInit flag (now removed). Added some more dodgy Spanish translations.
Ben Soares [Thu, 1 Nov 2018 14:27:00 +0000 (14:27 +0000)]
JAL-3141 Preferences 'Backups' tab now fits. Moved initial option setting into Preferences with all the other preference initial setting.
Ben Soares [Wed, 31 Oct 2018 17:04:19 +0000 (17:04 +0000)]
JAL-3141 Preferences 'Backups' tab now working. Doesn't fit in default space though -- needs adjusting
gmungoc [Thu, 25 Oct 2018 19:27:16 +0000 (20:27 +0100)]
JAL-3143 unit tests updated for code changes!
Ben Soares [Thu, 25 Oct 2018 15:36:41 +0000 (16:36 +0100)]
JAL-3141 Ostensibly all backups working for alignment and project saves. Need to add a preferences tab and some tests.
gmungoc [Thu, 25 Oct 2018 14:41:21 +0000 (15:41 +0100)]
JAL-3143 comma-delimited feature attributes for alleles,
clinical_significance
gmungoc [Thu, 25 Oct 2018 13:56:01 +0000 (14:56 +0100)]
JAL-3143 fetch Ensembl(Genomes) features as JSON not GFF
Ben Soares [Wed, 24 Oct 2018 12:23:27 +0000 (13:23 +0100)]
JAL-3141 Code checkout. Not compiling.
Ben Soares [Wed, 24 Oct 2018 12:22:50 +0000 (13:22 +0100)]
JAL-3141 Code checkout. Not compiling.
Ben Soares [Tue, 23 Oct 2018 17:03:52 +0000 (18:03 +0100)]
BackupFilter and other unfinished business
gmungoc [Tue, 23 Oct 2018 14:31:50 +0000 (15:31 +0100)]
JAL-3139 check group visibility when removing 'redundant' features
Ben Soares [Mon, 22 Oct 2018 16:10:38 +0000 (17:10 +0100)]
JAL-3141 Taken the backing up code out of FileChooser into its own class for more generic usage, and extra data safe-guarding functionality
Ben Soares [Mon, 22 Oct 2018 16:03:15 +0000 (17:03 +0100)]
JAL-3141 Taken the backing up code out of FileChooser into its own class for more generic usage, and extra data safe-guarding functionality
Ben Soares [Mon, 22 Oct 2018 09:25:09 +0000 (10:25 +0100)]
JAL-3141 Tidying
Ben Soares [Fri, 19 Oct 2018 16:26:27 +0000 (17:26 +0100)]
JAL-3141 Backup files being created with default suffix up to 10 backups. Configurable in .jalview_properties but no GUI for this yet.
Jim Procter [Tue, 16 Oct 2018 16:28:02 +0000 (17:28 +0100)]
JAL-3127 always look up sequence ID colour from view when colouring by Sequence ID
Jim Procter [Tue, 16 Oct 2018 16:23:07 +0000 (17:23 +0100)]
JAL-3127 tidy up terminology in colour schemes help text
Jim Procter [Tue, 16 Oct 2018 16:22:46 +0000 (17:22 +0100)]
JAL-3127 updated colours menu and tree view documentation
Jim Procter [Tue, 16 Oct 2018 16:20:51 +0000 (17:20 +0100)]
JAL-3127 reinstate ability to set sequence ID colour directly by right-clicking a node
Jim Procter [Tue, 16 Oct 2018 15:38:10 +0000 (16:38 +0100)]
JAL-3127 use AlignViewportI.addGroup to create & propagate groups to complement view and update structure views accordingly
Jim Procter [Tue, 16 Oct 2018 15:37:13 +0000 (16:37 +0100)]
JAL-3127 use AlignViewportI.addGroup() to add group and propagate to complement view. also updates sequence ID colours from group’s idColour attribute
Jim Procter [Tue, 16 Oct 2018 15:34:53 +0000 (16:34 +0100)]
viewport flag to indicate when structure view needs updating
JAL-3127 fix regression on JAL-868 due to JAL-2773
Jim Procter [Tue, 9 Oct 2018 12:31:19 +0000 (13:31 +0100)]
JAL-3127 Colour sequences by ID - need to check that group colours are properly propagated to structure view independently of shading by linked alignment by selecting from Structure Views colour menu.
Jim Procter [Tue, 9 Oct 2018 12:23:25 +0000 (13:23 +0100)]
JAL-3127 TODO - resolve reference to Viewport for group colour schemes instantiated before the viewport has been created.
Jim Procter [Tue, 9 Oct 2018 12:22:48 +0000 (13:22 +0100)]
JAL-3127 pass reference to AlignViewportI when creating an instance of ColourSchemeI
gmungoc [Mon, 8 Oct 2018 09:13:00 +0000 (10:13 +0100)]
JAL-1244 comments, javadoc, method signature tweaks
gmungoc [Mon, 8 Oct 2018 08:09:27 +0000 (09:09 +0100)]
JAL-1244 editSequence extract method refactoring
gmungoc [Fri, 5 Oct 2018 12:56:33 +0000 (13:56 +0100)]
JAL-1244 improved status message for insert/delete gap
gmungoc [Thu, 4 Oct 2018 13:54:40 +0000 (14:54 +0100)]
JAL-3132 status message for sequence and/or graph group annotation
gmungoc [Thu, 4 Oct 2018 13:14:48 +0000 (14:14 +0100)]
JAL-1244 no status message (yet) for locked edit of single sequence
gmungoc [Thu, 4 Oct 2018 13:08:58 +0000 (14:08 +0100)]
JAL-1244 status message for insert/delete gaps on single sequence
gmungoc [Thu, 4 Oct 2018 11:29:08 +0000 (12:29 +0100)]
JAL-1244 status message while dragging a stretch group
gmungoc [Thu, 4 Oct 2018 10:45:22 +0000 (11:45 +0100)]
JAL-3132 set status message when over sequence id or annotation label
gmungoc [Thu, 4 Oct 2018 10:38:48 +0000 (11:38 +0100)]
JAL-3093 unit tests, no mouse action over left/right wrapped scale
gmungoc [Wed, 3 Oct 2018 12:53:25 +0000 (13:53 +0100)]
JAL-3093 tweaks to code and test for 3px gap above annotations in
wrapped mode
gmungoc [Tue, 2 Oct 2018 16:08:07 +0000 (17:08 +0100)]
JAL-3093 unit tests for SeqPanel.findMousePosition
gmungoc [Tue, 2 Oct 2018 11:35:02 +0000 (12:35 +0100)]
JAL-3093 limited Consensus popup menu when in wrapped mode
gmungoc [Tue, 2 Oct 2018 07:52:50 +0000 (08:52 +0100)]
JAL-3093 added MousePos.isOverAnnotation() for extra clarity of
intention
gmungoc [Mon, 1 Oct 2018 16:22:33 +0000 (17:22 +0100)]
JAL-3093 'read-only' annotations when in wrapped mode
gmungoc [Mon, 1 Oct 2018 14:06:00 +0000 (15:06 +0100)]
JAL-3093 refactor (+test) Annotation Labels tooltip ready for reuse
gmungoc [Mon, 1 Oct 2018 14:05:28 +0000 (15:05 +0100)]
JAL-3093 unit tests for finding annotation row index for mouse pos
gmungoc [Mon, 1 Oct 2018 11:05:31 +0000 (12:05 +0100)]
JAL-3093 show annotation tooltips and status message in wrapped mode
gmungoc [Fri, 28 Sep 2018 11:29:55 +0000 (12:29 +0100)]
JAL-3063 service param files read/saved using JAXB not Castor binding
gmungoc [Fri, 28 Sep 2018 11:29:28 +0000 (12:29 +0100)]
JAL-3063 top level element added to JalviewWsParamSet.xsd
gmungoc [Fri, 28 Sep 2018 11:28:54 +0000 (12:28 +0100)]
JAL-3063 comments re use of xjc to generate Java binding classes
gmungoc [Thu, 27 Sep 2018 15:40:27 +0000 (16:40 +0100)]
JAL-2791 refactored Export Features to apply all visibility tests
gmungoc [Thu, 27 Sep 2018 15:39:51 +0000 (16:39 +0100)]
JAL-2791 new method to test if feature fails colour threshold test
gmungoc [Thu, 27 Sep 2018 15:23:16 +0000 (16:23 +0100)]
JAL-2791 method that tests all conditions for feature visibility
gmungoc [Wed, 26 Sep 2018 14:08:11 +0000 (15:08 +0100)]
JAL-3125 tidy up
gmungoc [Wed, 26 Sep 2018 11:05:01 +0000 (12:05 +0100)]
JAL-3125 avoid slider 'rounding' threshold field value
gmungoc [Mon, 24 Sep 2018 07:53:16 +0000 (08:53 +0100)]
JAL-3063 tidy commented out code
gmungoc [Fri, 21 Sep 2018 13:52:20 +0000 (14:52 +0100)]
JAL-3063 wrappers with check for null getting optional Integer, Float,
Boolean XML attributes
gmungoc [Fri, 21 Sep 2018 08:52:19 +0000 (09:52 +0100)]
JAL-3120 preserve feature colour/mincolour/maxcolour while modifying,
rationalise FeatureColour constructors
gmungoc [Thu, 20 Sep 2018 11:23:14 +0000 (12:23 +0100)]
JAL-2843 tweaks to help text for filters
gmungoc [Thu, 20 Sep 2018 10:54:31 +0000 (11:54 +0100)]
JAL-2843 help text for colour by attribute, feature filters
Jim Procter [Wed, 19 Sep 2018 14:45:29 +0000 (15:45 +0100)]
Merge branch 'bug/JAL-3120restoreFeatureColour' into develop
gmungoc [Wed, 19 Sep 2018 13:59:44 +0000 (14:59 +0100)]
JAL-3120 preserve plain colour value when changing to Colour by Label
gmungoc [Wed, 19 Sep 2018 12:44:58 +0000 (13:44 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 19 Sep 2018 11:39:17 +0000 (12:39 +0100)]
Merge branch 'cherrypick/JAL-2808_notabs' into develop
Jim Procter [Thu, 5 Jul 2018 13:38:42 +0000 (14:38 +0100)]
JAL-2808 JAL-3026 deleted all commented out tab code from the dialog
Omitted dialog refactoring from JAL-3058
gmungoc [Thu, 5 Jul 2018 13:27:44 +0000 (14:27 +0100)]
JAL-2808 JAL-3032 drop tabbed layout for Colours and Filters
gmungoc [Wed, 19 Sep 2018 08:07:49 +0000 (09:07 +0100)]
JAL-3063 use JAXB for 'Save as Project' and load project from parameter
gmungoc [Wed, 19 Sep 2018 07:03:38 +0000 (08:03 +0100)]
JAL-3063 unit test for save/load project switched to JAXB
gmungoc [Tue, 18 Sep 2018 16:43:03 +0000 (17:43 +0100)]
JAL-3063 Save/Load user defined colours using JAXB
gmungoc [Tue, 18 Sep 2018 15:58:25 +0000 (16:58 +0100)]
JAL-3063 Save/Load user colour scheme using JAXB
gmungoc [Tue, 18 Sep 2018 15:57:42 +0000 (16:57 +0100)]
JAL-3063 top level element added to colours schema, JAXB classes regen'd
gmungoc [Tue, 18 Sep 2018 15:18:13 +0000 (16:18 +0100)]
JAL-3063 New View via JAXB
gmungoc [Tue, 18 Sep 2018 15:03:09 +0000 (16:03 +0100)]
JAL-3063 temporary extra menu option to save/load project as JAXB
gmungoc [Tue, 18 Sep 2018 15:02:34 +0000 (16:02 +0100)]
JAL-3063 first version of Jalview2XML using JAXB to (un)marshal
gmungoc [Tue, 18 Sep 2018 15:01:52 +0000 (16:01 +0100)]
JAL-3063 JAXB binding classes generated by xjc from jalview.xsd
gmungoc [Tue, 18 Sep 2018 15:01:07 +0000 (16:01 +0100)]
JAL-3063 tweak schema so JAXB tool xjc recognises XML root element
gmungoc [Tue, 18 Sep 2018 15:00:20 +0000 (16:00 +0100)]
JAL-3063 tweak schema so JAXB generates enums for enumerated values
Jim Procter [Tue, 18 Sep 2018 14:40:39 +0000 (15:40 +0100)]
JAL-3035 more dedasification
Jim Procter [Tue, 18 Sep 2018 14:01:56 +0000 (15:01 +0100)]
JAL-2865 release notes
gmungoc [Mon, 17 Sep 2018 10:51:43 +0000 (11:51 +0100)]
JAL-3116 test method renamed to match code
gmungoc [Mon, 17 Sep 2018 10:47:51 +0000 (11:47 +0100)]
JAL-3116 unit tests adapted to EMBL over JAXB
gmungoc [Fri, 14 Sep 2018 16:11:40 +0000 (17:11 +0100)]
JAL-3116 parse EMBL XML with JAXB (todo: update unit tests)
gmungoc [Thu, 13 Sep 2018 15:28:27 +0000 (16:28 +0100)]
JAL-3116 Uniprot XML unmarshalled using JAXB not Castor
gmungoc [Wed, 12 Sep 2018 15:30:52 +0000 (16:30 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 12 Sep 2018 15:20:51 +0000 (16:20 +0100)]
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop
gmungoc [Wed, 12 Sep 2018 11:27:21 +0000 (12:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 12 Sep 2018 10:59:39 +0000 (11:59 +0100)]
JAL-1551 reinstated Save actions
Jim Procter [Tue, 11 Sep 2018 15:06:03 +0000 (16:06 +0100)]
JAL-3112 increased TEST_TIMEOUT to 9000ms - needed after inclusion discovered class path entries
Jim Procter [Tue, 11 Sep 2018 15:05:02 +0000 (16:05 +0100)]
JAL-3112 Use classgraph to reconstruct the classpath for launching Jalview
Jim Procter [Tue, 11 Sep 2018 13:05:00 +0000 (14:05 +0100)]
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop
Jim Procter [Tue, 11 Sep 2018 13:03:50 +0000 (14:03 +0100)]
JAL-3111 drop hts-1.33 as a dependency (in favour of htsjdk-2.12)
Jim Procter [Tue, 11 Sep 2018 12:56:41 +0000 (13:56 +0100)]
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop
Jim Procter [Tue, 11 Sep 2018 12:31:09 +0000 (13:31 +0100)]
Merge branch 'releases/Release_2_11_Branch' into merge/JAL-3091_develop_211
Jim Procter [Tue, 11 Sep 2018 12:29:37 +0000 (13:29 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch
JAL-3091 bring 2.11 onto release 2.10.5 to simplify merge
gmungoc [Mon, 10 Sep 2018 13:13:47 +0000 (14:13 +0100)]
JAL-3099 use Alignment.getVisibleWidth() where wanted
gmungoc [Mon, 10 Sep 2018 12:45:57 +0000 (13:45 +0100)]
JAL-3099 new method AlignmentI.getVisibleWidth()
gmungoc [Mon, 10 Sep 2018 10:29:11 +0000 (11:29 +0100)]
JAL-3097 adjust viewport width on hiding columns
gmungoc [Mon, 10 Sep 2018 09:34:21 +0000 (10:34 +0100)]
JAL-3108 fix concurrency bug in Reveal action handler
git://source.jalview.org / jalview.git / log