jalview.git
5 years agoJAL-3032 small formatting and isJS() tidy
gmungoc [Wed, 27 Mar 2019 16:29:29 +0000 (16:29 +0000)]
JAL-3032 small formatting and isJS() tidy

5 years agoreinstating test data for JalviewJS
hansonr [Wed, 27 Mar 2019 12:30:50 +0000 (08:30 -0400)]
reinstating test data for JalviewJS

5 years agocomment out of @j2sNative block
hansonr [Wed, 27 Mar 2019 11:33:59 +0000 (07:33 -0400)]
comment out of @j2sNative block

5 years agoallows web-page embedding
hansonr [Wed, 27 Mar 2019 11:00:52 +0000 (07:00 -0400)]
allows web-page embedding

5 years agoconsolidation of Platform isJS calls
hansonr [Wed, 27 Mar 2019 10:06:38 +0000 (06:06 -0400)]
consolidation of Platform isJS calls

5 years agoisJS cleanup
hansonr [Wed, 27 Mar 2019 09:40:22 +0000 (05:40 -0400)]
isJS cleanup

5 years agoclean-up of isJS business for (temporarily) noneditable JS JComboBox
hansonr [Wed, 27 Mar 2019 09:39:05 +0000 (05:39 -0400)]
clean-up of isJS business for (temporarily) noneditable JS JComboBox

5 years agoPlatform comment about isPopupTrigger Jalview-JS/developPreFrameEmbedding
hansonr [Wed, 27 Mar 2019 00:33:12 +0000 (20:33 -0400)]
Platform comment about isPopupTrigger

5 years agoupgraded Platform.java
hansonr [Tue, 26 Mar 2019 11:18:14 +0000 (07:18 -0400)]
upgraded Platform.java

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Mon, 25 Mar 2019 16:37:39 +0000 (16:37 +0000)]
Merge branch 'develop' into Jalview-JS/develop

5 years agoJAL-2717 adjusted code so default correctly returned if i18n fails
gmungoc [Mon, 25 Mar 2019 16:21:42 +0000 (16:21 +0000)]
JAL-2717 adjusted code so default correctly returned if i18n fails

5 years agoJAL-3127 scripts updated for method signature change
gmungoc [Mon, 25 Mar 2019 08:57:56 +0000 (08:57 +0000)]
JAL-3127 scripts updated for method signature change

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Sat, 23 Mar 2019 08:57:59 +0000 (08:57 +0000)]
Merge branch 'develop' into Jalview-JS/develop

5 years agoJAL-1889 explicit recalc of geometry for scale left/right/above on/off bug/JAL-1889serverTestSuite
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

5 years agoJAL-1889 remove debug logging, add updateLayout()
gmungoc [Sat, 23 Mar 2019 06:40:38 +0000 (06:40 +0000)]
JAL-1889 remove debug logging, add updateLayout()

5 years agoJAL-1889 more debug logging
gmungoc [Fri, 22 Mar 2019 14:38:08 +0000 (14:38 +0000)]
JAL-1889 more debug logging

5 years agoJAL-1889 better debug logging
gmungoc [Thu, 21 Mar 2019 16:28:40 +0000 (16:28 +0000)]
JAL-1889 better debug logging

5 years agoJAL-1889 temporary debug in findColumn()
gmungoc [Thu, 21 Mar 2019 15:59:39 +0000 (15:59 +0000)]
JAL-1889 temporary debug in findColumn()

5 years agoJAL-1889 added belt and braces deleteOnExit() to test output file
gmungoc [Thu, 21 Mar 2019 15:44:48 +0000 (15:44 +0000)]
JAL-1889 added belt and braces deleteOnExit() to test output file

5 years agoJAL-1889 correct props param, remove dasserver, output file paths
gmungoc [Thu, 21 Mar 2019 15:33:51 +0000 (15:33 +0000)]
JAL-1889 correct props param, remove dasserver, output file paths

5 years agoJAL-1889 more diagnostics for CommandLineOperations
gmungoc [Thu, 21 Mar 2019 13:26:14 +0000 (13:26 +0000)]
JAL-1889 more diagnostics for CommandLineOperations

5 years agoJAL-1889 diagnostics for failing test on server
gmungoc [Thu, 21 Mar 2019 10:12:06 +0000 (10:12 +0000)]
JAL-1889 diagnostics for failing test on server

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Wed, 20 Mar 2019 15:19:48 +0000 (15:19 +0000)]
Merge branch 'develop' into Jalview-JS/develop

Conflicts:
src/jalview/gui/AlignFrame.java
src/jalview/gui/ScalePanel.java

5 years agoJAL-3093 fine tuning of SeqPanel tooltip
gmungoc [Wed, 20 Mar 2019 14:35:34 +0000 (14:35 +0000)]
JAL-3093 fine tuning of SeqPanel tooltip

5 years agoJAL-3212 unit test and fix for Scale Panel bug
gmungoc [Wed, 20 Mar 2019 12:25:31 +0000 (12:25 +0000)]
JAL-3212 unit test and fix for Scale Panel bug

5 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
gmungoc [Wed, 20 Mar 2019 09:19:38 +0000 (09:19 +0000)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

5 years agoJAL-3210 code formatting only
gmungoc [Tue, 19 Mar 2019 15:40:21 +0000 (15:40 +0000)]
JAL-3210 code formatting only

5 years agoJAL-3192 corefile after loading in exampleFile_2_7.jvp
Jim Procter [Tue, 19 Mar 2019 15:37:04 +0000 (15:37 +0000)]
JAL-3192 corefile after loading in exampleFile_2_7.jvp

5 years agoJAL-1551 reinstate formatting and save actions (with Java 1.8 additions)
gmungoc [Mon, 18 Mar 2019 15:11:33 +0000 (15:11 +0000)]
JAL-1551 reinstate formatting and save actions (with Java 1.8 additions)

5 years agoJAL-3141 JAL-3056 backups regime option suppressed in JalviewJS
gmungoc [Mon, 18 Mar 2019 14:31:11 +0000 (14:31 +0000)]
JAL-3141 JAL-3056 backups regime option suppressed in JalviewJS

5 years agoJAL-3210 JAL-3063 JAL-3035 remove Castor and Spring libraries
gmungoc [Mon, 18 Mar 2019 10:39:10 +0000 (10:39 +0000)]
JAL-3210 JAL-3063 JAL-3035 remove Castor and Spring libraries

5 years agoJAL-3210 JAL-3140 intervalstore.jar in .classpath.js also
gmungoc [Mon, 18 Mar 2019 10:26:58 +0000 (10:26 +0000)]
JAL-3210 JAL-3140 intervalstore.jar in .classpath.js also

5 years agoJAL-3210 remove unnecessary (and malformed?) .classpath from .gitignore
gmungoc [Sun, 17 Mar 2019 11:00:44 +0000 (11:00 +0000)]
JAL-3210 remove unnecessary (and malformed?) .classpath from .gitignore

5 years agoJAL-3210 ensure tooltips on FeatureSettings in JS
gmungoc [Fri, 15 Mar 2019 15:55:31 +0000 (15:55 +0000)]
JAL-3210 ensure tooltips on FeatureSettings in JS

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Fri, 15 Mar 2019 14:58:30 +0000 (14:58 +0000)]
Merge branch 'develop' into Jalview-JS/develop

5 years agoJAL-2964 missed branch for restore link tree to all views
gmungoc [Fri, 15 Mar 2019 14:57:54 +0000 (14:57 +0000)]
JAL-2964 missed branch for restore link tree to all views

5 years agoMerge branch 'develop' into Jalview-JS/develop
gmungoc [Fri, 15 Mar 2019 14:18:19 +0000 (14:18 +0000)]
Merge branch 'develop' into Jalview-JS/develop

5 years agoJAL-3203 Overview show hidden default false also in Preferences
gmungoc [Fri, 15 Mar 2019 14:17:44 +0000 (14:17 +0000)]
JAL-3203 Overview show hidden default false also in Preferences

5 years agoJAL-3071 corrections to IdPanel$ScrollThread
gmungoc [Fri, 15 Mar 2019 09:08:01 +0000 (09:08 +0000)]
JAL-3071 corrections to IdPanel$ScrollThread

5 years agoJAL-2814 updated unit test for code change
gmungoc [Fri, 15 Mar 2019 08:04:46 +0000 (08:04 +0000)]
JAL-2814 updated unit test for code change

5 years agoJAL-2814 JAL-3032 targeted help URL links for JalviewJS
gmungoc [Thu, 14 Mar 2019 13:05:33 +0000 (13:05 +0000)]
JAL-2814 JAL-3032 targeted help URL links for JalviewJS

5 years agoJAL-3056 open Help web page instead of internal (targeted) help link
gmungoc [Thu, 14 Mar 2019 12:40:43 +0000 (12:40 +0000)]
JAL-3056 open Help web page instead of internal (targeted) help link

5 years agoJAL-3210 JAL-3141 JAL-3056 disable backups in JalviewJS
gmungoc [Thu, 14 Mar 2019 10:51:01 +0000 (10:51 +0000)]
JAL-3210 JAL-3141 JAL-3056 disable backups in JalviewJS

5 years agoJAL-3210 relocate setMinimumSize so it works in JS
gmungoc [Thu, 14 Mar 2019 10:05:07 +0000 (10:05 +0000)]
JAL-3210 relocate setMinimumSize so it works in JS

5 years agoJAL-3210 JAL-3140 intervalstore library added to JS as zip
gmungoc [Thu, 14 Mar 2019 08:39:15 +0000 (08:39 +0000)]
JAL-3210 JAL-3140 intervalstore library added to JS as zip

5 years agoJAL-3210 merge conflict tidying
gmungoc [Wed, 13 Mar 2019 15:54:42 +0000 (15:54 +0000)]
JAL-3210 merge conflict tidying

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