gmungoc [Mon, 11 Mar 2019 16:32:45 +0000 (16:32 +0000)]
Merge branch 'develop' into merge/JAL-3127
gmungoc [Mon, 11 Mar 2019 16:30:12 +0000 (16:30 +0000)]
JAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test AfterMethod!
gmungoc [Mon, 11 Mar 2019 15:36:36 +0000 (15:36 +0000)]
JAL-3127 fix faulty merge
gmungoc [Mon, 11 Mar 2019 15:07:39 +0000 (15:07 +0000)]
Merge branch 'develop' into merge/JAL-3127
Conflicts:
src/jalview/viewmodel/AlignmentViewport.java
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 11:37:58 +0000 (11:37 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
Conflicts:
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
test/jalview/io/Jalview2xmlTests.java
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
Jim Procter [Thu, 7 Mar 2019 14:25:41 +0000 (14:25 +0000)]
JAL-3127 set ‘updateStructures’ flag for viewports associated with each tree to true when groups are deleted, rather then when we create new groups (which may not always be the case).
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
git://source.jalview.org / jalview.git / log