jalview

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Commits this week: 8
Total Committers: 73
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Commits this week: 8

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Thursday 09 Jul 2020
3:58 pm

Jim Procter

Merge branch 'alpha/merge_212_JalviewJS_2112' into spike/JAL-3622_Scanner_swingjs_J212_merge

Options
3:43 pm

Mateusz Warowny

Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/merge_212_JalviewJS_2112

Conflicts:

src/jalview/gui/Desktop.java

src/jalview/gui/Preferences.java

src/jalview/jbgui/GPreferences.java

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    • -13
    • +13
    /src/jalview/gui/AlignFrame.java
    • -10
    • +30
    /src/jalview/gui/Desktop.java
    • -1
    • +5
    /src/jalview/gui/Preferences.java
    • -0
    • +4
    /src/jalview/jbgui/GPreferences.java
    • -7
    • +16
    /src/jalview/ws/jws2/Jws2Discoverer.java
Wednesday 08 Jul 2020
3:27 pm

Mateusz Warowny

JAL-3683 retrieve job status to output stream

Options
    • -25
    • +18
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
12:59 pm

Mateusz Warowny

JAL-6386 update slivka client for j2s compatibility

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    • binary
    /j11lib/slivka-client.jar
    • -11
    • +4
    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Tuesday 23 Jun 2020
5:21 pm

Jim Procter

JAL-3622 update with swingJS from hansonr1

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    • binary
    /swingjs/SwingJS-site.zip
    • binary
    /swingjs/net.sf.j2s.core-j11.jar
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • -1
    • +1
    /swingjs/ver/3.2.9-j11/timestamp
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/ver/3.2.9/timestamp
Monday 18 May 2020
3:26 pm

Jim Procter

Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/AlignViewportI.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceI.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/JvSwingUtils.java

src/jalview/gui/OverviewPanel.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SplitFrame.java

src/jalview/gui/WsJobParameters.java

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/FileLoader.java

src/jalview/io/StockholmFile.java

src/jalview/jbgui/GAlignFrame.java

src/jalview/jbgui/GPreferences.java

src/jalview/renderer/AnnotationRenderer.java

src/jalview/viewmodel/AlignmentViewport.java

src/jalview/ws/jws2/Jws2Discoverer.java

test/jalview/analysis/AAFrequencyTest.java

test/jalview/gui/AlignFrameTest.java

test/jalview/gui/AlignViewportTest.java

Options
    • -3
    • +89
    /resources/lang/Messages.properties
    • -1
    • +1
    /resources/lang/Messages_es.properties
    • -24
    • +246
    /src/jalview/analysis/AAFrequency.java
    • -0
    • +88
    /src/jalview/analysis/AlignmentSorter.java
    • -18
    • +21
    /src/jalview/analysis/AlignmentUtils.java
    • -1
    • +0
    /src/jalview/analysis/Dna.java
    • -4
    • +26
    /src/jalview/api/AlignViewportI.java
    • -0
    • +33
    /src/jalview/appletgui/AlignFrame.java
    • -20
    • +8
    /src/jalview/appletgui/AlignViewport.java
    • -2
    • +2
    /src/jalview/appletgui/AlignmentPanel.java
    • -1
    • +0
    /src/jalview/appletgui/AnnotationPanel.java
    • -1
    • +1
    /src/jalview/appletgui/OverviewPanel.java
    • -4
    • +1
    /src/jalview/appletgui/TitledPanel.java
    • -24
    • +24
    /src/jalview/bin/Jalview.java
    • -20
    • +76
    /src/jalview/datamodel/Alignment.java
  16. … 60 more files in changeset.
11:01 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3529 test updated for revised signature of getDBRefs()

Options
    • -13
    • +15
    /test/jalview/io/StockholmFileTest.java
10:59 am

gmungoc <g.m.carstairs@dundee.ac.uk>

Merge branch 'Jalview-JS/develop' into develop

Conflicts:

build.gradle

src/jalview/gui/PopupMenu.java

src/jalview/io/SequenceAnnotationReport.java

src/jalview/io/StockholmFile.java

src/jalview/util/DBRefUtils.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

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    • -1
    • +1
    /src/jalview/appletgui/APopupMenu.java
    • -2
    • +2
    /src/jalview/datamodel/features/FeatureAttributes.java
    • -44
    • +6
    /src/jalview/ext/ensembl/EnsemblInfo.java
    • -56
    • +22
    /src/jalview/ext/ensembl/EnsemblMap.java
    • -1
    • +1
    /src/jalview/gui/APQHandlers.java
    • -31
    • +100
    /src/jalview/gui/IdPanel.java
    • -113
    • +162
    /src/jalview/gui/PopupMenu.java
    • -93
    • +195
    /src/jalview/gui/SeqPanel.java
    • -1
    • +2
    /src/jalview/io/BackupFiles.java
    • -3
    • +3
    /src/jalview/io/FeaturesFile.java
    • -22
    • +19
    /src/jalview/io/SequenceAnnotationReport.java
    • -51
    • +54
    /src/jalview/io/StockholmFile.java
    • -1
    • +1
    /src/jalview/io/vcf/VCFLoader.java
    • -1
    • +1
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
    • -526
    • +529
    /src/jalview/util/DBRefUtils.java
  16. … 5 more files in changeset.

changeset discussion

  1. Jim Procter: relevant issue is JAL-3626
9:39 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3613 remove debug code committed in error

Options
    • -5
    • +1
    /src/jalview/util/BrowserLauncher.java
Friday 01 May 2020
12:36 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3613 check sequence overlap when matching search results

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    • -3
    • +7
    /src/jalview/datamodel/SearchResults.java
    • -7
    • +8
    /src/jalview/gui/SeqPanel.java
    • -1
    • +5
    /src/jalview/util/BrowserLauncher.java
    • -2
    • +66
    /test/jalview/datamodel/SearchResultsTest.java
Thursday 23 Apr 2020
6:54 pm

Jim Procter

Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha update for 2.11.1 release

Options
    • -0
    • +3
    /help/help/help.jhm
    • -1
    • +3
    /help/help/helpTOC.xml
    • -0
    • +9
    /resources/lang/Messages.properties
    • -1
    • +3
    /resources/lang/Messages_es.properties
    • -113
    • +26
    /src/jalview/analysis/AlignmentUtils.java
    • -1
    • +22
    /src/jalview/appletgui/AlignFrame.java
    • -1
    • +18
    /src/jalview/bin/Jalview.java
    • -9
    • +1
    /src/jalview/datamodel/Sequence.java
    • -3
    • +50
    /src/jalview/gui/AlignFrame.java
    • -6
    • +5
    /src/jalview/gui/AlignViewport.java
    • -1
    • +1
    /src/jalview/gui/AnnotationLabels.java
    • -2
    • +0
    /src/jalview/gui/AssociatePdbFileWithSeq.java
    • -2
    • +0
    /src/jalview/gui/CalculationChooser.java
    • -2
    • +48
    /src/jalview/gui/Desktop.java
    • -1
    • +0
    /src/jalview/gui/EditNameDialog.java
  16. … 28 more files in changeset.
6:41 pm

Jim Procter

Merge branch 'alpha/JAL-3066_Jalview_212_slivka-integration' into alpha/JAL-3362_Jalview_212_alpha

Options
Wednesday 22 Apr 2020
8:58 pm

Ben Soares

JAL-3225 save auto formatting settings in org.eclipse.jdt.ui.prefs. Not yet put into place, but these settings should be used

Options
    • -0
    • +67
    /utils/eclipse/org.eclipse.jdt.ui.prefs
12:07 am

Jim Procter

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

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12:06 am

Jim Procter

JAL-3407 add GPL license to Jalview source files

Options
    • -0
    • +20
    /src/jalview/analysis/GeneticCodeI.java
    • -0
    • +20
    /src/jalview/analysis/GeneticCodes.java
    • -0
    • +20
    /src/jalview/api/FinderI.java
    • -0
    • +20
    /src/jalview/bin/GetMemory.java
    • -0
    • +20
    /src/jalview/bin/JalviewTaskbar.java
    • -0
    • +20
    /src/jalview/bin/Launcher.java
    • -0
    • +20
    /src/jalview/bin/MemorySetting.java
    • -0
    • +20
    /src/jalview/datamodel/GeneLociI.java
    • -0
    • +20
    /src/jalview/datamodel/GeneLocus.java
    • -0
    • +20
    /src/jalview/datamodel/MappedFeatures.java
    • -0
    • +20
    /src/jalview/datamodel/Point.java
    • -0
    • +20
    /src/jalview/datamodel/features/FeatureAttributeType.java
    • -0
    • +20
    /src/jalview/datamodel/features/FeatureAttributes.java
    • -0
    • +20
    /src/jalview/datamodel/features/FeatureMatcher.java
    • -0
    • +20
    /src/jalview/datamodel/features/FeatureMatcherI.java
  16. … 29 more files in changeset.
12:03 am

Jim Procter

JAL-3407 release notes - JAL-247 - for auto-set-ID, and revise wording for transferring virtual features in chimera

Options
    • -3
    • +10
    /help/help/html/releases.html
Tuesday 21 Apr 2020
9:19 pm

Jim Procter

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

Options
9:18 pm

Jim Procter

JAL-3407 fix JAL-3574 - remove from known issues for 2.11.1.0

Options
    • -3
    • +0
    /help/help/html/releases.html
6:23 pm

Jim Procter

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

Options
6:23 pm

Jim Procter

JAL-3574 JAL-3407 release notes

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    • -0
    • +3
    /help/help/html/releases.html
6:06 pm

Jim Procter

Merge branch 'bug/JAL-3574filterByPOS' into documentation/JAL-3407_2.11.1_release

Options
6:03 pm

Jim Procter

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

Options
5:39 pm

Jim Procter

JAL-3407 add and document ComputePeptideVariants.groovy

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    • -0
    • +32
    /examples/groovy/ComputePeptideVariants.groovy
    • -0
    • +18
    /help/help/html/features/importvcf.html
    • -0
    • +5
    /help/help/html/releases.html
    • -1
    • +7
    /help/help/html/whatsNew.html
3:37 pm

Ben Soares

JAL-3577 changed default RELEASE dir in build.gradle to use absolute path to help buildship when importing project for first time

Options
    • -1
    • +1
    /build.gradle
2:16 pm

Jim Procter

Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

Options
2:10 pm

Jim Procter

JAL-3567 JAL-3407 document sequence features report and the additional info provided for virtual features. Also bumped release date to 22st April

Options
    • -0
    • +1
    /help/help/help.jhm
    • -0
    • +1
    /help/help/helpTOC.xml
    • -0
    • +54
    /help/help/html/features/seqfeaturereport.html
    • binary
    /help/help/html/features/seqfeaturesrep.png
    • -3
    • +7
    /help/help/html/features/splitView.html
    • -3
    • +15
    /help/help/html/menus/popupMenu.html
    • -3
    • +3
    /help/help/html/releases.html
2:03 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3210 try adding setup method to unit test failing on server...

Options
    • -12
    • +32
    /test/jalview/gui/SeqCanvasTest.java
12:34 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1889 corrected wait for consensus to be calculated

Options
    • -19
    • +20
    /test/jalview/gui/AlignFrameTest.java
    • -10
    • +21
    /test/jalview/gui/AlignViewportTest.java
    • -9
    • +6
    /test/jalview/gui/AlignmentPanelTest.java
    • -13
    • +10
    /test/jalview/schemes/PIDColourSchemeTest.java
12:07 pm

Ben Soares

JAL-3577 Added newer install dirs to the deletion list in the uninstaller and tidied the list

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    • -29
    • +49
    /utils/install4j/install4j8_template.install4j
11:58 am

Jim Procter

Merge branch 'bug/JAL-3567virtualFeatureCoordinates' into develop

Options