gmungoc [Mon, 11 Mar 2019 15:04:23 +0000 (15:04 +0000)]
Merge branch 'feature/JAL-2250colourAllGroups' into develop
gmungoc [Mon, 11 Mar 2019 14:54:26 +0000 (14:54 +0000)]
JAL-3201 restore group colours correctly from project
gmungoc [Mon, 11 Mar 2019 08:50:41 +0000 (08:50 +0000)]
JAL-3206 strict above/below threshold test restored
gmungoc [Mon, 11 Mar 2019 08:45:18 +0000 (08:45 +0000)]
Merge branch 'bug/JAL-3075' into develop
gmungoc [Fri, 8 Mar 2019 14:37:26 +0000 (14:37 +0000)]
JAL-3193 defensive trim of URL read from properties file
gmungoc [Fri, 8 Mar 2019 11:55:15 +0000 (11:55 +0000)]
JAL-2903 typos fixed
gmungoc [Fri, 8 Mar 2019 11:26:52 +0000 (11:26 +0000)]
JAL-3075 update column selection on mouse up after scroll
gmungoc [Thu, 7 Mar 2019 16:12:25 +0000 (16:12 +0000)]
Merge branch 'feature/JAL-3180colourAnnotationMenu' into merge/JAL-3180
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
gmungoc [Thu, 7 Mar 2019 15:08:15 +0000 (15:08 +0000)]
JAL-2250 default Apply Colour to All Groups selected
gmungoc [Thu, 7 Mar 2019 12:57:28 +0000 (12:57 +0000)]
JAL-2717 JAL-2360 belated unit tests for ColourMenuHelper
gmungoc [Tue, 21 Aug 2018 12:59:37 +0000 (13:59 +0100)]
JAL-2717 corrected i18n of colour scheme names
gmungoc [Thu, 7 Mar 2019 09:14:33 +0000 (09:14 +0000)]
Merge branch 'feature/JAL-3205symmetricCalc' into develop
gmungoc [Thu, 7 Mar 2019 08:43:44 +0000 (08:43 +0000)]
JAL-3035 removed spring libraries as only used for jdas
gmungoc [Wed, 6 Mar 2019 16:01:34 +0000 (16:01 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 16:01:12 +0000 (16:01 +0000)]
JAL-3035 restored erroneous deletion
gmungoc [Wed, 6 Mar 2019 15:50:20 +0000 (15:50 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 15:49:46 +0000 (15:49 +0000)]
JAL-3035 more das bits removed
gmungoc [Tue, 5 Mar 2019 17:57:54 +0000 (17:57 +0000)]
Merge branch 'bug/JAL-3201groupClustal' into develop
gmungoc [Tue, 5 Mar 2019 16:44:20 +0000 (16:44 +0000)]
Merge remote-tracking branch 'origin/features/JAL-2620alternativeCodeTables' into merge/JAL-2620
gmungoc [Tue, 5 Mar 2019 15:22:40 +0000 (15:22 +0000)]
Merge branch 'bug/JAL-2621' into develop
Conflicts:
src/jalview/gui/OverviewPanel.java
gmungoc [Tue, 5 Mar 2019 15:07:51 +0000 (15:07 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-3141_Messages_discrepancy_fix' into develop
gmungoc [Tue, 5 Mar 2019 12:40:08 +0000 (12:40 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2839findWithHidden' into merge/JAL-2839_2933
gmungoc [Tue, 5 Mar 2019 12:05:28 +0000 (12:05 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-914multipleHelpScreens' into develop
gmungoc [Tue, 5 Mar 2019 12:01:37 +0000 (12:01 +0000)]
Merge remote-tracking branch 'origin/features/JAL-2814ftsHelp' into merge/JAL-2814
Ben Soares [Tue, 5 Mar 2019 11:44:27 +0000 (11:44 +0000)]
JAL-3141 Fixed inconsistent (changed) message labels in Messages_es.props and changed a label in props and code for consistency/avoid confusion
gmungoc [Tue, 5 Mar 2019 11:20:44 +0000 (11:20 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-3002fastPaintWrapped' into develop
gmungoc [Wed, 22 Aug 2018 10:31:04 +0000 (11:31 +0100)]
JAL-3049 JAL-3032 tidy/i18n code, remove redundant tooltip registration
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/gui/FeatureSettings.java
gmungoc [Tue, 5 Mar 2019 10:26:53 +0000 (10:26 +0000)]
JAL-3049 redo (part of) commit 92bc328
gmungoc [Fri, 6 Jul 2018 09:55:46 +0000 (10:55 +0100)]
JAL-3054 small y-overlap of tooltip and cell leads the eye better
gmungoc [Tue, 5 Mar 2019 09:01:48 +0000 (09:01 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-3049colourCellTooltip' into
merge/JAL-3049
Conflicts:
src/jalview/api/FeatureColourI.java
src/jalview/schemes/FeatureColour.java
test/jalview/schemes/FeatureColourTest.java
gmungoc [Tue, 5 Mar 2019 08:15:29 +0000 (08:15 +0000)]
JAL-3205 added a delta parameter to Matrix.equals()
gmungoc [Mon, 4 Mar 2019 17:06:13 +0000 (17:06 +0000)]
Merge branch 'bug/JAL-3072scrollThread' into merge/JAL-3072_3073
Conflicts:
src/jalview/datamodel/Alignment.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqPanel.java
gmungoc [Mon, 4 Mar 2019 16:44:19 +0000 (16:44 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-3082selectRegex' into merge/JAL-3082
gmungoc [Mon, 4 Mar 2019 16:22:40 +0000 (16:22 +0000)]
JAL-3206 avoid divide by zero when threshold is graphMin / graphMax
gmungoc [Mon, 4 Mar 2019 12:30:09 +0000 (12:30 +0000)]
Merge branch 'bug/JAL-3099alignmentVisibleWidth' into merge/JAL-3099
Conflicts:
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/IdCanvas.java
test/jalview/datamodel/AlignmentTest.java
gmungoc [Mon, 4 Mar 2019 11:47:14 +0000 (11:47 +0000)]
Merge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into merge/JAL-3035
gmungoc [Mon, 4 Mar 2019 10:54:27 +0000 (10:54 +0000)]
Merge branch 'bug/JAL-3120restoreFeatureColour' into merge/JAL-3120
Conflicts:
src/jalview/gui/Jalview2XML.java
test/jalview/io/Jalview2xmlTests.java
gmungoc [Mon, 4 Mar 2019 09:19:22 +0000 (09:19 +0000)]
JAL-3205 worked examples in unit test for symmetric/asymmetric matrix
gmungoc [Sun, 3 Mar 2019 08:40:40 +0000 (08:40 +0000)]
JAL-3205 one more unit test case
gmungoc [Sun, 3 Mar 2019 07:25:25 +0000 (07:25 +0000)]
JAL-3205 faster calculation with symmetric score matrix
gmungoc [Fri, 1 Mar 2019 15:35:54 +0000 (15:35 +0000)]
Merge branch 'bug/JAL-2791exportFilteredFeature' into merge/JAL-2791
gmungoc [Fri, 1 Mar 2019 15:12:06 +0000 (15:12 +0000)]
Merge branch 'feature/JAL-3093wrappedModeTooltips' into merge/JAL-3093_JAL-3132
gmungoc [Fri, 1 Mar 2019 15:11:31 +0000 (15:11 +0000)]
JAL-3093 unit test adapts to actual number of annotation rows
gmungoc [Fri, 1 Mar 2019 14:30:03 +0000 (14:30 +0000)]
Merge branch 'feature/JAL-3093wrappedModeTooltips' into
merge/JAL-3093_JAL-3132
Conflicts:
src/jalview/gui/SeqPanel.java
test/jalview/gui/SeqPanelTest.java
gmungoc [Fri, 1 Mar 2019 12:26:45 +0000 (12:26 +0000)]
Merge branch 'feature/JAL-1244stretchStatusMsg' into merge/JAL-1244
Conflicts:
src/jalview/commands/EditCommand.java
gmungoc [Fri, 1 Mar 2019 12:12:04 +0000 (12:12 +0000)]
Merge branch 'bug/JAL-3139colocatedFeatures' into develop
gmungoc [Fri, 1 Mar 2019 11:23:39 +0000 (11:23 +0000)]
JAL-3154 disable reorder columns before adding to viewport
gmungoc [Fri, 1 Mar 2019 11:17:11 +0000 (11:17 +0000)]
Merge branch 'bug/JAL-3154tableColumnDrag' into develop
gmungoc [Fri, 1 Mar 2019 11:00:39 +0000 (11:00 +0000)]
Merge branch 'bug/JAL-3161annotationTooltipRange' into develop
gmungoc [Fri, 1 Mar 2019 10:57:17 +0000 (10:57 +0000)]
Merge branch 'bug/JAL-3158selectionBroadcasts' into merge/JAL-3158
gmungoc [Fri, 1 Mar 2019 10:07:54 +0000 (10:07 +0000)]
Merge branch 'bug/JAL-3164complementOverview' into merge/JAL-3164
gmungoc [Fri, 1 Mar 2019 10:00:28 +0000 (10:00 +0000)]
Merge branch 'merge/JAL-3140' into develop
gmungoc [Fri, 1 Mar 2019 09:59:24 +0000 (09:59 +0000)]
JAL-3140 update for change to SequenceI api
gmungoc [Fri, 1 Mar 2019 09:41:58 +0000 (09:41 +0000)]
Merge branch 'feature/intervalStoreJ' into merge/JAL-3140
gmungoc [Fri, 1 Mar 2019 09:23:11 +0000 (09:23 +0000)]
JAL-3140 reduced coupling to intervalstore.jar
gmungoc [Thu, 28 Feb 2019 16:41:55 +0000 (16:41 +0000)]
JAL-3140 confine intervalstore imports to jalview.datamodel.features
gmungoc [Thu, 28 Feb 2019 15:59:02 +0000 (15:59 +0000)]
Merge branch 'bug/JAL-2420revealAllMenu' into develop
gmungoc [Thu, 28 Feb 2019 15:58:47 +0000 (15:58 +0000)]
Merge branch 'bug/JAL-3166npeAllRowsHidden' into develop
gmungoc [Thu, 28 Feb 2019 15:51:18 +0000 (15:51 +0000)]
Merge branch 'feature/JAL-3169cancelOverwrite' into develop
Conflicts:
src/jalview/io/JalviewFileChooser.java
Jim Procter [Thu, 28 Feb 2019 15:31:19 +0000 (15:31 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
gmungoc [Thu, 28 Feb 2019 15:15:21 +0000 (15:15 +0000)]
Merge branch 'feature/JAL-3143ensemblJSON' into merge/JAL-3143
gmungoc [Thu, 28 Feb 2019 14:15:43 +0000 (14:15 +0000)]
Merge remote-tracking branch 'origin/feature/JAL-3141_backupfiles_for211' into merge/JAL3141
Jim Procter [Thu, 28 Feb 2019 13:46:48 +0000 (13:46 +0000)]
Merge branch 'feature/JAL-3141_backupfiles_for211' into develop
gmungoc [Wed, 27 Feb 2019 15:36:23 +0000 (15:36 +0000)]
JAL-2527 default Overview 'hide hidden' i.e. WYSIWYG
gmungoc [Tue, 26 Feb 2019 11:39:34 +0000 (11:39 +0000)]
JAL-3201 JAL-2386 don't pre-select 'apply to all groups'
gmungoc [Tue, 26 Feb 2019 10:41:05 +0000 (10:41 +0000)]
JAL-3201 group colour schemes distinct instances
gmungoc [Mon, 25 Feb 2019 13:46:27 +0000 (13:46 +0000)]
JAL-3200 fast lookup of DSSP3 notation
gmungoc [Sun, 24 Feb 2019 08:58:51 +0000 (08:58 +0000)]
JAL-3198 don't recalculate group conservation for Id Panel selection
gmungoc [Sun, 24 Feb 2019 08:10:17 +0000 (08:10 +0000)]
JAL-3198 SequenceGroup 'bulk constructor' without duplicates check
gmungoc [Fri, 22 Feb 2019 11:27:59 +0000 (11:27 +0000)]
JAL-2915 don't recalculate Overview on scroll to position, ever!
gmungoc [Fri, 22 Feb 2019 10:04:02 +0000 (10:04 +0000)]
JAL-2738 don't set AF as feature score
Ben Soares [Fri, 22 Feb 2019 09:19:53 +0000 (09:19 +0000)]
JAL-3141 improved message for asking whether to delete files (file modification time and size added to info to help user decide
Ben Soares [Thu, 21 Feb 2019 17:59:25 +0000 (17:59 +0000)]
JAL-3141 Sensible refactoring for confirming deleting 'newer' old backup files
Ben Soares [Sun, 17 Feb 2019 18:19:42 +0000 (18:19 +0000)]
JAL-3141 User warning when deleting old backup files that are newer than the previous backup file
Ben Soares [Fri, 15 Feb 2019 19:38:34 +0000 (19:38 +0000)]
JAL-3141 re-order deletion of old files and check lastModified times with their replacements
Ben Soares [Thu, 14 Feb 2019 15:52:03 +0000 (15:52 +0000)]
JAL-3141 Added warning/confirmation when suffixReverse is changed without changing suffixTemplate or suffixDigits (Bad Things might happen to previous backup files)
Ben Soares [Thu, 14 Feb 2019 14:20:13 +0000 (14:20 +0000)]
JAL-3141 Moved 'Previously saved scheme' combo box preference out to 'Cancel changes' button. Tidied up the Summary box display.
gmungoc [Thu, 7 Feb 2019 11:41:02 +0000 (11:41 +0000)]
JAL-3140 updated to latest intervalstore.jar
gmungoc [Mon, 4 Feb 2019 12:18:29 +0000 (12:18 +0000)]
JAL-3143 update unit test for ID -> id change
Ben Soares [Fri, 1 Feb 2019 09:42:13 +0000 (09:42 +0000)]
JAL-3141 Slight efficiency gain in detecting backupfiles in the File Chooser
Ben Soares [Wed, 30 Jan 2019 10:10:42 +0000 (10:10 +0000)]
JAL-3141 Enabled the 'Include backpup files' checkbox for loading alignments from local file
Ben Soares [Tue, 29 Jan 2019 14:15:51 +0000 (14:15 +0000)]
JAL-3141 Found a good fix for updating the FileChooser list of files when 'Include backup files' checkbox is checked/unchecked.
Ben Soares [Tue, 29 Jan 2019 11:41:52 +0000 (11:41 +0000)]
JAL-3141 Found a (not ideal) fix for updating the FileChooser list of files when 'Include backup files' checkbox is checked/unchecked.
gmungoc [Tue, 29 Jan 2019 11:17:48 +0000 (11:17 +0000)]
JAL-3143 format alleles array for feature description
Ben Soares [Mon, 28 Jan 2019 10:53:32 +0000 (10:53 +0000)]
JAL-3141 improvement on BackupFilenameParts filename matching
Ben Soares [Mon, 28 Jan 2019 10:06:11 +0000 (10:06 +0000)]
JAL-3141 fixed test
Ben Soares [Fri, 25 Jan 2019 17:32:37 +0000 (17:32 +0000)]
JAL-3141. This adds quite a lot of code to allow an 'Include backup files' checkbox in the 'Load Project' JalviewFileChooser. However I cannot for the life of me get the file list in the FileChooser to refresh /reliably/ on a mac at least anyway (it does about 1 time in 9git status).
Ben Soares [Thu, 24 Jan 2019 16:54:21 +0000 (16:54 +0000)]
JAL-3141 Added a '.fa' to filename examples
Ben Soares [Thu, 24 Jan 2019 16:47:43 +0000 (16:47 +0000)]
JAL-3141 Change of label (change of '_' character to ' ')
Ben Soares [Thu, 24 Jan 2019 16:33:11 +0000 (16:33 +0000)]
JAL-3141 Change of label
Ben Soares [Thu, 24 Jan 2019 16:25:26 +0000 (16:25 +0000)]
JAL-3141 Removed border around example filenames in Backups Preferences pane
Ben Soares [Thu, 24 Jan 2019 15:56:58 +0000 (15:56 +0000)]
JAL-3141 New layout and wording of Backups Preferences pane after consultation with SD. Seriously rationalised 'backupfiles...SetEnable' to allow for more complex widget enabling/disabling depending on other widget values. Fixed a buglet or two when there's an unusual selection of options (when suffix has no '%n' or is completely empty).
Ben Soares [Thu, 24 Jan 2019 15:29:54 +0000 (15:29 +0000)]
JAL-3141 Eclipse re-formatting of file
gmungoc [Thu, 24 Jan 2019 14:30:31 +0000 (14:30 +0000)]
JAL-3018 Ensembl version updated to 9.0
Ben Soares [Thu, 24 Jan 2019 09:37:05 +0000 (09:37 +0000)]
JAL-3141 Reformatted code in eclipse
Ben Soares [Wed, 23 Jan 2019 20:33:20 +0000 (20:33 +0000)]
JAL-3141 Added Presets options in the Backups Preferences pane, with several presets available and sensible 'Default' option chosen first time.
gmungoc [Wed, 23 Jan 2019 09:15:52 +0000 (09:15 +0000)]
JAL-3063 correct handling of absent choice element in DBRef Mapping
Ben Soares [Tue, 22 Jan 2019 13:15:08 +0000 (13:15 +0000)]
JAL-3141 Fixed what happens when suffix template has no '%n' index
Ben Soares [Tue, 22 Jan 2019 13:14:06 +0000 (13:14 +0000)]
JAL-3141 New message translations
Ben Soares [Mon, 21 Jan 2019 22:56:41 +0000 (22:56 +0000)]
JAL-3141 Rejigged the Preferences tab and changed some text
git://source.jalview.org / jalview.git / log