gmungoc [Thu, 21 Nov 2019 13:09:19 +0000 (13:09 +0000)]
JAL-3484 temporary override of autocalc preferences for project load
gmungoc [Thu, 21 Nov 2019 13:06:35 +0000 (13:06 +0000)]
JAL-3485 (enum) constants for Auto-annotation label and preference key
gmungoc [Thu, 21 Nov 2019 10:43:21 +0000 (10:43 +0000)]
JAL-3081 test and fix for preserve annotation order on New View
gmungoc [Tue, 19 Nov 2019 14:26:47 +0000 (14:26 +0000)]
JAL-3484 tests for load project with changed autocalc Preferences
gmungoc [Sun, 17 Nov 2019 13:38:27 +0000 (13:38 +0000)]
JAL-3081 sort annotations by order read from project after reloading
gmungoc [Fri, 15 Nov 2019 14:58:53 +0000 (14:58 +0000)]
JAL-3081 refactored AnnotationSorter constructor and sort parameters
gmungoc [Fri, 15 Nov 2019 14:58:09 +0000 (14:58 +0000)]
JAL-3199 corrected sort menu items to JMenuItem
gmungoc [Fri, 15 Nov 2019 14:56:48 +0000 (14:56 +0000)]
JAL-3081 is/setShowAutocalculatedAbove pulled up to interface
gmungoc [Thu, 14 Nov 2019 16:56:00 +0000 (16:56 +0000)]
JAL-3081 compiler warnings and formatting improvements
gmungoc [Thu, 14 Nov 2019 16:13:31 +0000 (16:13 +0000)]
JAL-3081 unit tests for 'custom' (no) sort, sort autocalc only
gmungoc [Thu, 14 Nov 2019 16:01:29 +0000 (16:01 +0000)]
JAL-3081 autocalculated annotation first/last leaves others unchanged
gmungoc [Thu, 14 Nov 2019 15:03:16 +0000 (15:03 +0000)]
JAL-3199 sort annotations after adding from annotation file
gmungoc [Thu, 14 Nov 2019 14:28:20 +0000 (14:28 +0000)]
JAL-3199 'Sort Annotations by...' now a one-off action, not a 'state'
gmungoc [Thu, 14 Nov 2019 14:26:18 +0000 (14:26 +0000)]
JAL-3199 sort annotations after adding from web service
gmungoc [Thu, 14 Nov 2019 14:25:45 +0000 (14:25 +0000)]
JAL-3199 promote sortAnnotations to AlignmentViewPanel
gmungoc [Fri, 8 Nov 2019 09:37:12 +0000 (09:37 +0000)]
JAL-3081 restore annotation ordering from project (work in progress)
gmungoc [Fri, 8 Nov 2019 09:36:52 +0000 (09:36 +0000)]
JAL-3081 more efficient algorithm for annotation ordering by sequence
gmungoc [Fri, 8 Nov 2019 09:35:44 +0000 (09:35 +0000)]
JAL-3081 new method to get alignment sequence order lookup
gmungoc [Fri, 8 Nov 2019 09:35:01 +0000 (09:35 +0000)]
JAL-3081 promote setSortAnnotationsBy() to api method
gmungoc [Fri, 8 Nov 2019 09:32:22 +0000 (09:32 +0000)]
JAL-3081 schema and binding class changes to save annotation sort order
gmungoc [Wed, 3 Apr 2019 13:44:57 +0000 (14:44 +0100)]
JAL-3199 apply annotation sorting on AlignFrame construction
gmungoc [Wed, 3 Apr 2019 13:07:37 +0000 (14:07 +0100)]
JAL-3081 JAL-3199 no auto-sort of annotations after manual reordering
gmungoc [Fri, 29 Mar 2019 11:05:29 +0000 (11:05 +0000)]
JAL-3140 InstallAnywhere updated to intervalstore-v1.0.jar
gmungoc [Fri, 29 Mar 2019 10:31:02 +0000 (10:31 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 Mar 2019 10:30:51 +0000 (10:30 +0000)]
JAL-3140 intervalstore now v1.0 (public release)
Jim Procter [Fri, 29 Mar 2019 09:54:49 +0000 (09:54 +0000)]
JAL-3111 Disable the pubapplet target in build.xml so cruisecontrol build can complete
Jim Procter [Thu, 28 Mar 2019 17:34:20 +0000 (17:34 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 28 Mar 2019 17:34:11 +0000 (17:34 +0000)]
JAL-3111 biojava dependencies
Jim Procter [Thu, 28 Mar 2019 17:20:31 +0000 (17:20 +0000)]
JAL-3111 fix libquagua dependency paths - needs to be checked on OSX InstallAnywhere
Jim Procter [Thu, 28 Mar 2019 17:20:04 +0000 (17:20 +0000)]
JAL-3111 fix jabaws dependency name in IA config
Jim Procter [Thu, 28 Mar 2019 16:59:51 +0000 (16:59 +0000)]
JAL-3111 intervalstore library on IA classpath
gmungoc [Thu, 28 Mar 2019 16:13:39 +0000 (16:13 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Thu, 28 Mar 2019 15:55:08 +0000 (15:55 +0000)]
JAL-3111 typo in IA config
gmungoc [Thu, 28 Mar 2019 15:52:34 +0000 (15:52 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 28 Mar 2019 15:52:23 +0000 (15:52 +0000)]
JAL-1889 patch for failing isControDown test on build server
Jim Procter [Thu, 28 Mar 2019 15:40:20 +0000 (15:40 +0000)]
JAL-3111 update InstallAnywhere dependencies for changed libraries
gmungoc [Thu, 28 Mar 2019 07:56:40 +0000 (07:56 +0000)]
Merge branch 'feature/JAL-3181linkOrdering' into develop
gmungoc [Wed, 27 Mar 2019 17:06:12 +0000 (17:06 +0000)]
JAL-2620 improved error reporting on failure to load resource files
gmungoc [Mon, 25 Mar 2019 16:21:42 +0000 (16:21 +0000)]
JAL-2717 adjusted code so default correctly returned if i18n fails
gmungoc [Mon, 25 Mar 2019 08:57:56 +0000 (08:57 +0000)]
JAL-3127 scripts updated for method signature change
gmungoc [Sat, 23 Mar 2019 08:49:52 +0000 (08:49 +0000)]
JAL-1889 explicit recalc of geometry for scale left/right/above on/off
gmungoc [Sat, 23 Mar 2019 06:40:38 +0000 (06:40 +0000)]
JAL-1889 remove debug logging, add updateLayout()
gmungoc [Fri, 22 Mar 2019 14:38:08 +0000 (14:38 +0000)]
JAL-1889 more debug logging
gmungoc [Thu, 21 Mar 2019 16:28:40 +0000 (16:28 +0000)]
JAL-1889 better debug logging
gmungoc [Thu, 21 Mar 2019 15:59:39 +0000 (15:59 +0000)]
JAL-1889 temporary debug in findColumn()
gmungoc [Thu, 21 Mar 2019 15:44:48 +0000 (15:44 +0000)]
JAL-1889 added belt and braces deleteOnExit() to test output file
gmungoc [Thu, 21 Mar 2019 15:33:51 +0000 (15:33 +0000)]
JAL-1889 correct props param, remove dasserver, output file paths
gmungoc [Thu, 21 Mar 2019 13:26:14 +0000 (13:26 +0000)]
JAL-1889 more diagnostics for CommandLineOperations
gmungoc [Thu, 21 Mar 2019 10:12:06 +0000 (10:12 +0000)]
JAL-1889 diagnostics for failing test on server
gmungoc [Wed, 20 Mar 2019 14:35:34 +0000 (14:35 +0000)]
JAL-3093 fine tuning of SeqPanel tooltip
gmungoc [Wed, 20 Mar 2019 12:25:31 +0000 (12:25 +0000)]
JAL-3212 unit test and fix for Scale Panel bug
gmungoc [Fri, 15 Mar 2019 14:57:54 +0000 (14:57 +0000)]
JAL-2964 missed branch for restore link tree to all views
gmungoc [Fri, 15 Mar 2019 14:17:44 +0000 (14:17 +0000)]
JAL-3203 Overview show hidden default false also in Preferences
gmungoc [Tue, 12 Mar 2019 09:04:21 +0000 (09:04 +0000)]
JAL-1270 missing 'alwaysRun=true' added to setup/teardown
gmungoc [Tue, 12 Mar 2019 08:18:42 +0000 (08:18 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
gmungoc [Tue, 12 Mar 2019 08:18:07 +0000 (08:18 +0000)]
JAL-3127 check for null viewport
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
git://source.jalview.org / jalview.git / log