jalview.git
5 years agoJAL-1889 hack to ensure endRes is computed in setUp
gmungoc [Wed, 13 Mar 2019 11:57:54 +0000 (11:57 +0000)]
JAL-1889 hack to ensure endRes is computed in setUp

5 years agoJAL-3141 fix up merge artefact so BackupFilesTest passes
gmungoc [Wed, 13 Mar 2019 10:50:39 +0000 (10:50 +0000)]
JAL-3141 fix up merge artefact so BackupFilesTest passes

5 years agoMerge branch 'develop' into trialMerge
gmungoc [Wed, 13 Mar 2019 09:26:03 +0000 (09:26 +0000)]
Merge branch 'develop' into trialMerge

Conflicts:
.classpath
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/api/AlignViewportI.java
src/jalview/fts/core/GFTSPanel.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/IdPanel.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqPanel.java
src/jalview/io/JalviewFileChooser.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GFinder.java
src/jalview/jbgui/GPCAPanel.java
src/jalview/util/DBRefUtils.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
test/jalview/io/CrossRef2xmlTests.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/ws/dbsources/UniprotTest.java

5 years agoJAL-1270 missing 'alwaysRun=true' added to setup/teardown
gmungoc [Tue, 12 Mar 2019 09:04:21 +0000 (09:04 +0000)]
JAL-1270 missing 'alwaysRun=true' added to setup/teardown

5 years agoMerge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
gmungoc [Tue, 12 Mar 2019 08:18:42 +0000 (08:18 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127

5 years agoJAL-3127 check for null viewport feature/JAL-3127_seqidChainshading
gmungoc [Tue, 12 Mar 2019 08:18:07 +0000 (08:18 +0000)]
JAL-3127 check for null viewport

5 years agoMerge branch 'develop' into merge/JAL-3127
gmungoc [Mon, 11 Mar 2019 16:32:45 +0000 (16:32 +0000)]
Merge branch 'develop' into merge/JAL-3127

5 years agoJAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test AfterMethod!
gmungoc [Mon, 11 Mar 2019 16:30:12 +0000 (16:30 +0000)]
JAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test AfterMethod!

5 years agoJAL-3127 fix faulty merge
gmungoc [Mon, 11 Mar 2019 15:36:36 +0000 (15:36 +0000)]
JAL-3127 fix faulty merge

5 years agoMerge branch 'develop' into merge/JAL-3127
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

5 years agoMerge branch 'feature/JAL-2250colourAllGroups' into develop
gmungoc [Mon, 11 Mar 2019 15:04:23 +0000 (15:04 +0000)]
Merge branch 'feature/JAL-2250colourAllGroups' into develop

5 years agoJAL-3201 restore group colours correctly from project feature/JAL-2250colourAllGroups
gmungoc [Mon, 11 Mar 2019 14:54:26 +0000 (14:54 +0000)]
JAL-3201 restore group colours correctly from project

5 years agoMerge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
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

5 years agoJAL-3206 strict above/below threshold test restored
gmungoc [Mon, 11 Mar 2019 08:50:41 +0000 (08:50 +0000)]
JAL-3206 strict above/below threshold test restored

5 years agoMerge branch 'bug/JAL-3075' into develop
gmungoc [Mon, 11 Mar 2019 08:45:18 +0000 (08:45 +0000)]
Merge branch 'bug/JAL-3075' into develop

5 years agoJAL-3193 defensive trim of URL read from properties file
gmungoc [Fri, 8 Mar 2019 14:37:26 +0000 (14:37 +0000)]
JAL-3193 defensive trim of URL read from properties file

5 years agoJAL-2903 typos fixed
gmungoc [Fri, 8 Mar 2019 11:55:15 +0000 (11:55 +0000)]
JAL-2903 typos fixed

5 years agoJAL-3075 update column selection on mouse up after scroll bug/JAL-3075
gmungoc [Fri, 8 Mar 2019 11:26:52 +0000 (11:26 +0000)]
JAL-3075 update column selection on mouse up after scroll

5 years agoMerge branch 'feature/JAL-3180colourAnnotationMenu' into merge/JAL-3180
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

5 years agoJAL-2250 default Apply Colour to All Groups selected
gmungoc [Thu, 7 Mar 2019 15:08:15 +0000 (15:08 +0000)]
JAL-2250  default Apply Colour to All Groups selected

5 years agoJAL-3127 set ‘updateStructures’ flag for viewports associated with each tree to true...
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).

5 years agoJAL-2717 JAL-2360 belated unit tests for ColourMenuHelper
gmungoc [Thu, 7 Mar 2019 12:57:28 +0000 (12:57 +0000)]
JAL-2717 JAL-2360 belated unit tests for ColourMenuHelper

5 years agoJAL-2717 corrected i18n of colour scheme names
gmungoc [Tue, 21 Aug 2018 12:59:37 +0000 (13:59 +0100)]
JAL-2717 corrected i18n of colour scheme names

5 years agoMerge branch 'feature/JAL-3205symmetricCalc' into develop
gmungoc [Thu, 7 Mar 2019 09:14:33 +0000 (09:14 +0000)]
Merge branch 'feature/JAL-3205symmetricCalc' into develop

5 years agoJAL-3035 removed spring libraries as only used for jdas
gmungoc [Thu, 7 Mar 2019 08:43:44 +0000 (08:43 +0000)]
JAL-3035 removed spring libraries as only used for jdas

5 years agoMerge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 16:01:34 +0000 (16:01 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

5 years agoJAL-3035 restored erroneous deletion tasks/JAL-3035_remove_dasobert_dependency
gmungoc [Wed, 6 Mar 2019 16:01:12 +0000 (16:01 +0000)]
JAL-3035 restored erroneous deletion

5 years agoMerge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 15:50:20 +0000 (15:50 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

5 years agoJAL-3035 more das bits removed
gmungoc [Wed, 6 Mar 2019 15:49:46 +0000 (15:49 +0000)]
JAL-3035 more das bits removed

5 years agoJAL-3208 re-enable the setprop CLI arg, but only in JalviewJS
Jim Procter [Wed, 6 Mar 2019 15:29:34 +0000 (15:29 +0000)]
JAL-3208 re-enable the setprop CLI arg, but only in JalviewJS

5 years agoMerge branch 'bug/JAL-3201groupClustal' into develop
gmungoc [Tue, 5 Mar 2019 17:57:54 +0000 (17:57 +0000)]
Merge branch 'bug/JAL-3201groupClustal' into develop

5 years agoMerge remote-tracking branch 'origin/features/JAL-2620alternativeCodeTables' into...
gmungoc [Tue, 5 Mar 2019 16:44:20 +0000 (16:44 +0000)]
Merge remote-tracking branch 'origin/features/JAL-2620alternativeCodeTables' into merge/JAL-2620

5 years agoMerge branch 'bug/JAL-2621' into develop
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

5 years agoMerge remote-tracking branch 'origin/bug/JAL-3141_Messages_discrepancy_fix' into...
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

5 years agoMerge remote-tracking branch 'origin/bug/JAL-2839findWithHidden' into merge/JAL-2839_2933
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

5 years agoMerge remote-tracking branch 'origin/bug/JAL-914multipleHelpScreens' into develop
gmungoc [Tue, 5 Mar 2019 12:05:28 +0000 (12:05 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-914multipleHelpScreens' into develop

5 years agoMerge remote-tracking branch 'origin/features/JAL-2814ftsHelp' into merge/JAL-2814
gmungoc [Tue, 5 Mar 2019 12:01:37 +0000 (12:01 +0000)]
Merge remote-tracking branch 'origin/features/JAL-2814ftsHelp' into merge/JAL-2814

5 years agoJAL-3141 Fixed inconsistent (changed) message labels in Messages_es.props and changed... bug/JAL-3141_Messages_discrepancy_fix
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

5 years agoMerge remote-tracking branch 'origin/bug/JAL-3002fastPaintWrapped' into develop
gmungoc [Tue, 5 Mar 2019 11:20:44 +0000 (11:20 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-3002fastPaintWrapped' into develop

5 years agoJAL-3049 JAL-3032 tidy/i18n code, remove redundant tooltip registration
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

5 years agoJAL-3049 redo (part of) commit 92bc328
gmungoc [Tue, 5 Mar 2019 10:26:53 +0000 (10:26 +0000)]
JAL-3049 redo (part of) commit 92bc328

5 years agoJAL-3054 small y-overlap of tooltip and cell leads the eye better
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

5 years agoMerge remote-tracking branch 'origin/bug/JAL-3049colourCellTooltip' into
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

5 years agoJAL-3205 added a delta parameter to Matrix.equals() feature/JAL-3205symmetricCalc
gmungoc [Tue, 5 Mar 2019 08:15:29 +0000 (08:15 +0000)]
JAL-3205 added a delta parameter to Matrix.equals()

5 years agoMerge branch 'bug/JAL-3072scrollThread' into merge/JAL-3072_3073
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

5 years agoMerge remote-tracking branch 'origin/bug/JAL-3082selectRegex' into merge/JAL-3082
gmungoc [Mon, 4 Mar 2019 16:44:19 +0000 (16:44 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-3082selectRegex' into merge/JAL-3082

5 years agoJAL-3206 avoid divide by zero when threshold is graphMin / graphMax
gmungoc [Mon, 4 Mar 2019 16:22:40 +0000 (16:22 +0000)]
JAL-3206 avoid divide by zero when threshold is graphMin / graphMax

5 years agoMerge branch 'bug/JAL-3099alignmentVisibleWidth' into merge/JAL-3099
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

5 years agoMerge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into...
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

5 years agoMerge branch 'bug/JAL-3120restoreFeatureColour' into merge/JAL-3120
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

5 years agoJAL-3205 worked examples in unit test for symmetric/asymmetric matrix
gmungoc [Mon, 4 Mar 2019 09:19:22 +0000 (09:19 +0000)]
JAL-3205 worked examples in unit test for symmetric/asymmetric matrix

5 years agoJAL-3205 one more unit test case
gmungoc [Sun, 3 Mar 2019 08:40:40 +0000 (08:40 +0000)]
JAL-3205 one more unit test case

5 years agoJAL-3205 faster calculation with symmetric score matrix
gmungoc [Sun, 3 Mar 2019 07:25:25 +0000 (07:25 +0000)]
JAL-3205 faster calculation with symmetric score matrix

5 years agoMerge branch 'bug/JAL-2791exportFilteredFeature' into merge/JAL-2791
gmungoc [Fri, 1 Mar 2019 15:35:54 +0000 (15:35 +0000)]
Merge branch 'bug/JAL-2791exportFilteredFeature' into merge/JAL-2791

5 years agoMerge branch 'feature/JAL-3093wrappedModeTooltips' into merge/JAL-3093_JAL-3132
gmungoc [Fri, 1 Mar 2019 15:12:06 +0000 (15:12 +0000)]
Merge branch 'feature/JAL-3093wrappedModeTooltips' into merge/JAL-3093_JAL-3132

5 years agoJAL-3093 unit test adapts to actual number of annotation rows feature/JAL-3093wrappedModeTooltips
gmungoc [Fri, 1 Mar 2019 15:11:31 +0000 (15:11 +0000)]
JAL-3093 unit test adapts to actual number of annotation rows

5 years agoMerge branch 'feature/JAL-3093wrappedModeTooltips' into
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

5 years agoMerge branch 'tasks/JAL-3192_automateJalviewJScoreBuilding' into Jalview-JS/develop
Jim Procter [Fri, 1 Mar 2019 13:42:35 +0000 (13:42 +0000)]
Merge branch 'tasks/JAL-3192_automateJalviewJScoreBuilding' into Jalview-JS/develop

5 years agoJAL-3192 finally, make a JalviewJS_corename.html inside site for each core
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

5 years agoJAL-3192 don’t pass full path of classlist file as name of core file!
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!

5 years agoJAL-3192 call buildcore.xml:make-all-cores as part of JalviewJS site build
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

5 years agoJAL-3192 new build-all-cores target which iterates through all classlists/.txt files...
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

5 years agoMerge branch 'feature/JAL-1244stretchStatusMsg' into merge/JAL-1244
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

5 years agoMerge branch 'bug/JAL-3139colocatedFeatures' into develop
gmungoc [Fri, 1 Mar 2019 12:12:04 +0000 (12:12 +0000)]
Merge branch 'bug/JAL-3139colocatedFeatures' into develop

5 years agoJAL-3154 disable reorder columns before adding to viewport
gmungoc [Fri, 1 Mar 2019 11:23:39 +0000 (11:23 +0000)]
JAL-3154 disable reorder columns before adding to viewport

5 years agoMerge branch 'bug/JAL-3154tableColumnDrag' into develop
gmungoc [Fri, 1 Mar 2019 11:17:11 +0000 (11:17 +0000)]
Merge branch 'bug/JAL-3154tableColumnDrag' into develop

5 years agoMerge branch 'bug/JAL-3161annotationTooltipRange' into develop
gmungoc [Fri, 1 Mar 2019 11:00:39 +0000 (11:00 +0000)]
Merge branch 'bug/JAL-3161annotationTooltipRange' into develop

5 years agoMerge branch 'bug/JAL-3158selectionBroadcasts' into merge/JAL-3158
gmungoc [Fri, 1 Mar 2019 10:57:17 +0000 (10:57 +0000)]
Merge branch 'bug/JAL-3158selectionBroadcasts' into merge/JAL-3158

5 years agoMerge branch 'bug/JAL-3164complementOverview' into merge/JAL-3164
gmungoc [Fri, 1 Mar 2019 10:07:54 +0000 (10:07 +0000)]
Merge branch 'bug/JAL-3164complementOverview' into merge/JAL-3164

5 years agoMerge branch 'merge/JAL-3140' into develop
gmungoc [Fri, 1 Mar 2019 10:00:28 +0000 (10:00 +0000)]
Merge branch 'merge/JAL-3140' into develop

5 years agoJAL-3140 update for change to SequenceI api
gmungoc [Fri, 1 Mar 2019 09:59:24 +0000 (09:59 +0000)]
JAL-3140 update for change to SequenceI api

5 years agoMerge branch 'feature/intervalStoreJ' into merge/JAL-3140
gmungoc [Fri, 1 Mar 2019 09:41:58 +0000 (09:41 +0000)]
Merge branch 'feature/intervalStoreJ' into merge/JAL-3140

5 years agoJAL-3140 reduced coupling to intervalstore.jar feature/intervalStoreJ
gmungoc [Fri, 1 Mar 2019 09:23:11 +0000 (09:23 +0000)]
JAL-3140 reduced coupling to intervalstore.jar

5 years agoJAL-3140 confine intervalstore imports to jalview.datamodel.features
gmungoc [Thu, 28 Feb 2019 16:41:55 +0000 (16:41 +0000)]
JAL-3140 confine intervalstore imports to jalview.datamodel.features

5 years agoMerge branch 'bug/JAL-2420revealAllMenu' into develop
gmungoc [Thu, 28 Feb 2019 15:59:02 +0000 (15:59 +0000)]
Merge branch 'bug/JAL-2420revealAllMenu' into develop

5 years agoMerge branch 'bug/JAL-3166npeAllRowsHidden' into develop
gmungoc [Thu, 28 Feb 2019 15:58:47 +0000 (15:58 +0000)]
Merge branch 'bug/JAL-3166npeAllRowsHidden' into develop

5 years agoMerge branch 'feature/JAL-3169cancelOverwrite' 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

5 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Thu, 28 Feb 2019 15:31:19 +0000 (15:31 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

5 years agoMerge branch 'feature/JAL-3143ensemblJSON' into merge/JAL-3143
gmungoc [Thu, 28 Feb 2019 15:15:21 +0000 (15:15 +0000)]
Merge branch 'feature/JAL-3143ensemblJSON' into merge/JAL-3143

5 years agoMerge remote-tracking branch 'origin/feature/JAL-3141_backupfiles_for211' into merge...
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

5 years agoMerge branch 'feature/JAL-3141_backupfiles_for211' into develop merge/develop_feature/JAL-3141_backupfiles_for211
Jim Procter [Thu, 28 Feb 2019 13:46:48 +0000 (13:46 +0000)]
Merge branch 'feature/JAL-3141_backupfiles_for211' into develop

5 years agoJAL-3032 any url parameter not "j2s..." taken as Jalview args Jalview-BH/JAL-3026-JAL-3063-JAXB
gmungoc [Thu, 28 Feb 2019 12:42:46 +0000 (12:42 +0000)]
JAL-3032 any url parameter not "j2s..." taken as Jalview args

5 years agoJAL-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

5 years agoJAL-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

5 years agoJAL-3202 reduced scope of rendering flags
gmungoc [Wed, 27 Feb 2019 15:33:49 +0000 (15:33 +0000)]
JAL-3202 reduced scope of rendering flags

5 years agoJAL-3202 discard zero percentages in extracted profile
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

5 years agoJAL-3201 JAL-2386 don't pre-select 'apply to all groups'
gmungoc [Tue, 26 Feb 2019 11:39:34 +0000 (11:39 +0000)]
JAL-3201 JAL-2386 don't pre-select 'apply to all groups'

5 years agoJAL-3201 group colour schemes distinct instances
gmungoc [Tue, 26 Feb 2019 10:41:05 +0000 (10:41 +0000)]
JAL-3201 group colour schemes distinct instances

5 years agoJAL-3032 Jalview (as JS) parse query params to main arguments
gmungoc [Mon, 25 Feb 2019 15:54:48 +0000 (15:54 +0000)]
JAL-3032 Jalview (as JS) parse query params to main arguments

5 years agoJAL-3032 JalviewJS2 converts url query parameters to 'applet' args
gmungoc [Mon, 25 Feb 2019 15:24:57 +0000 (15:24 +0000)]
JAL-3032 JalviewJS2 converts url query parameters to 'applet' args

5 years agoJAL-3200 fast lookup of DSSP3 notation
gmungoc [Mon, 25 Feb 2019 13:46:27 +0000 (13:46 +0000)]
JAL-3200 fast lookup of DSSP3 notation

5 years agoJAL-3198 don't recalculate group conservation for Id Panel selection
gmungoc [Sun, 24 Feb 2019 08:58:51 +0000 (08:58 +0000)]
JAL-3198 don't recalculate group conservation for Id Panel selection

5 years agoJAL-3198 SequenceGroup 'bulk constructor' without duplicates check
gmungoc [Sun, 24 Feb 2019 08:10:17 +0000 (08:10 +0000)]
JAL-3198 SequenceGroup 'bulk constructor' without duplicates check

5 years agoJAL-2915 don't recalculate Overview on scroll to position, ever!
gmungoc [Fri, 22 Feb 2019 11:27:59 +0000 (11:27 +0000)]
JAL-2915 don't recalculate Overview on scroll to position, ever!

5 years agoJAL-2738 don't set AF as feature score
gmungoc [Fri, 22 Feb 2019 10:04:02 +0000 (10:04 +0000)]
JAL-2738 don't set AF as feature score

5 years agoJAL-3141 improved message for asking whether to delete files (file modification time...
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

5 years agoJAL-3141 Sensible refactoring for confirming deleting 'newer' old backup files
Ben Soares [Thu, 21 Feb 2019 17:59:25 +0000 (17:59 +0000)]
JAL-3141 Sensible refactoring for confirming deleting 'newer' old backup files

5 years agoJAL-3141 User warning when deleting old backup files that are newer than the previous...
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

5 years agoJAL-3141 re-order deletion of old files and check lastModified times with their repla...
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

5 years agoJAL-3141 Added warning/confirmation when suffixReverse is changed without changing...
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)