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
Jim Procter [Fri, 1 Mar 2019 13:42:35 +0000 (13:42 +0000)]
Merge branch 'tasks/JAL-3192_automateJalviewJScoreBuilding' into Jalview-JS/develop
Jim Procter [Fri, 1 Mar 2019 13:39:24 +0000 (13:39 +0000)]
JAL-3192 finally, make a JalviewJS_corename.html inside site for each core
Jim Procter [Fri, 1 Mar 2019 13:18:35 +0000 (13:18 +0000)]
JAL-3192 don’t pass full path of classlist file as name of core file!
Jim Procter [Fri, 1 Mar 2019 12:51:07 +0000 (12:51 +0000)]
JAL-3192 call buildcore.xml:make-all-cores as part of JalviewJS site build
Jim Procter [Fri, 1 Mar 2019 12:50:20 +0000 (12:50 +0000)]
JAL-3192 new build-all-cores target which iterates through all classlists/.txt files in it in order to build corefiles
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 [Thu, 28 Feb 2019 12:42:46 +0000 (12:42 +0000)]
JAL-3032 any url parameter not "j2s..." taken as Jalview args
gmungoc [Wed, 27 Feb 2019 15:36:23 +0000 (15:36 +0000)]
JAL-2527 default Overview 'hide hidden' i.e. WYSIWYG
gmungoc [Wed, 27 Feb 2019 15:36:23 +0000 (15:36 +0000)]
JAL-2527 default Overview 'hide hidden' i.e. WYSIWYG
gmungoc [Wed, 27 Feb 2019 15:33:49 +0000 (15:33 +0000)]
JAL-3202 reduced scope of rendering flags
gmungoc [Wed, 27 Feb 2019 12:31:04 +0000 (12:31 +0000)]
JAL-3202 discard zero percentages in extracted profile
Conflicts:
src/jalview/renderer/AnnotationRenderer.java
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 15:54:48 +0000 (15:54 +0000)]
JAL-3032 Jalview (as JS) parse query params to main arguments
gmungoc [Mon, 25 Feb 2019 15:24:57 +0000 (15:24 +0000)]
JAL-3032 JalviewJS2 converts url query parameters to 'applet' args
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 [Tue, 12 Feb 2019 10:37:54 +0000 (10:37 +0000)]
JAL-3032 default Autosearch to off for JalviewJS
gmungoc [Thu, 7 Feb 2019 11:41:02 +0000 (11:41 +0000)]
JAL-3140 updated to latest intervalstore.jar
hansonr [Tue, 5 Feb 2019 16:20:14 +0000 (10:20 -0600)]
latest transpiler and runtime
gmungoc [Tue, 5 Feb 2019 14:31:07 +0000 (14:31 +0000)]
JAL-3032 check enough sequences selected on construction
gmungoc [Tue, 5 Feb 2019 13:51:22 +0000 (13:51 +0000)]
Test (passes!) for dialog message truncation
gmungoc [Tue, 5 Feb 2019 13:36:49 +0000 (13:36 +0000)]
JAL-3048 JS-compatible confirm dialog on delete all
hansonr [Mon, 4 Feb 2019 17:17:11 +0000 (11:17 -0600)]
JSON parsing from a StringInputStream
hansonr [Mon, 4 Feb 2019 15:14:59 +0000 (09:14 -0600)]
SequenceFetcher JvCacheableInputBox isJS test
hansonr [Mon, 4 Feb 2019 14:52:01 +0000 (08:52 -0600)]
*new transpiler* and runtime.
hansonr [Mon, 4 Feb 2019 14:51:36 +0000 (08:51 -0600)]
refactoring for DBMODList
hansonr [Mon, 4 Feb 2019 14:50:46 +0000 (08:50 -0600)]
MIG -- explicitly sets Java9 switch to true for SwingJS
hansonr [Mon, 4 Feb 2019 14:49:55 +0000 (08:49 -0600)]
explicitly sets MIG platform defaults to WINDOWS_XP
hansonr [Mon, 4 Feb 2019 14:49:12 +0000 (08:49 -0600)]
adds protype size to JTextArea hack for nonexistent SwingJS editable
combo box
hansonr [Mon, 4 Feb 2019 14:48:05 +0000 (08:48 -0600)]
fixing array processing order
- does point out an issue with hiddenColumns joining adjacent hides
sometimes but not other times.
hansonr [Mon, 4 Feb 2019 14:46:42 +0000 (08:46 -0600)]
re-transpiled MIGLayout; JS-adapted AnnotationColumnChooser
hansonr [Mon, 4 Feb 2019 14:45:20 +0000 (08:45 -0600)]
Test suite try/catch reverted
hansonr [Mon, 4 Feb 2019 14:43:41 +0000 (08:43 -0600)]
unused - could be trashed.
hansonr [Mon, 4 Feb 2019 14:39:55 +0000 (08:39 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Mon, 4 Feb 2019 13:46:14 +0000 (13:46 +0000)]
Merge branch 'feature/JAL-3143ensemblJSON' into Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Mon, 4 Feb 2019 12:18:29 +0000 (12:18 +0000)]
JAL-3143 update unit test for ID -> id change
hansonr [Fri, 1 Feb 2019 13:45:25 +0000 (07:45 -0600)]
fix for org.json.JSONObject writing (both in Java and JavaScript)
hansonr [Fri, 1 Feb 2019 13:44:50 +0000 (07:44 -0600)]
removes unnecessary org.xml.sax; these are in SwingJS
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
hansonr [Thu, 31 Jan 2019 06:29:21 +0000 (00:29 -0600)]
Split pane removing title bar for JInternalFrames
hansonr [Thu, 31 Jan 2019 00:11:41 +0000 (18:11 -0600)]
fixes org.json.JSONObject for fully qualified method signatures
hansonr [Thu, 31 Jan 2019 00:11:06 +0000 (18:11 -0600)]
removes org.json from srcjar
gmungoc [Wed, 30 Jan 2019 16:05:51 +0000 (16:05 +0000)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of
https://source.jalview.org/git/jalview.git into
Jalview-BH/JAL-3026-JAL-3063-JAXB
Conflicts:
src/jalview/gui/SequenceFetcher.java
gmungoc [Wed, 30 Jan 2019 15:40:53 +0000 (15:40 +0000)]
JAL-3144 don't change comma to semi-colon if not requested!
hansonr [Wed, 30 Jan 2019 15:26:02 +0000 (09:26 -0600)]
woops.
hansonr [Wed, 30 Jan 2019 14:57:38 +0000 (08:57 -0600)]
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026-JAL-3063-JAXB
git://source.jalview.org / jalview.git / log