jalview

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Commits this week: 12
Total Committers: 60
Last Commit:
Commits this week: 12

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Today
4 hrs ago

Ben Soares

JAL-3141 Sensible refactoring for confirming deleting 'newer' old backup files

Options
    • -2
    • +8
    /resources/lang/Messages.properties
    • -2
    • +8
    /resources/lang/Messages_es.properties
    • -188
    • +227
    /src/jalview/io/BackupFiles.java
7 hrs ago

Mungo Carstairs

JAL-3187 handle no mapping / complement features without NPE

Options
    • -0
    • +4
    /src/jalview/datamodel/MappedFeatures.java
    • -5
    • +11
    /src/jalview/gui/SeqPanel.java
    • -7
    • +13
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
    • -4
    • +9
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
Wednesday 20 Feb
4:40 pm

Mungo Carstairs

Merge branch 'feature/JAL-3143ensemblJSON' into feature/JAL-3187linkedFeatures

Options
    • -5
    • +8
    /src/jalview/analysis/AlignmentUtils.java
    • -6
    • +10
    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
12:15 pm

Mungo Carstairs

JAL-3187 read peptide variant from CSQ:HGVSp if present (VCF/VEP data)

Options
    • -3
    • +24
    /src/jalview/datamodel/MappedFeatures.java
Tuesday 19 Feb
12:01 pm

Mungo Carstairs

Merge branch 'feature/JAL-3187linkedFeatures' into merge/JAL-3187_JAL-3010

Conflicts:

src/jalview/gui/FeatureSettings.java

src/jalview/renderer/seqfeatures/FeatureRenderer.java

Options
    • -0
    • +6
    /src/jalview/gui/FeatureSettings.java
11:15 am

Mungo Carstairs

JAL-3187 hacks to get peptide variant in to Jmol hover tooltip

Options
    • -1
    • +2
    /src/jalview/analysis/AlignmentUtils.java
    • -2
    • +2
    /src/jalview/appletgui/SeqPanel.java
    • -0
    • +154
    /src/jalview/datamodel/MappedFeatures.java
    • -9
    • +26
    /src/jalview/ext/jmol/JalviewJmolBinding.java
    • -4
    • +75
    /src/jalview/gui/SeqPanel.java
    • -4
    • +5
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
    • -1
    • +9
    /src/jalview/structure/SequenceListener.java
    • -6
    • +13
    /src/jalview/structure/StructureSelectionManager.java
    • -4
    • +26
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
Monday 18 Feb
9:19 am

Mungo Carstairs

JAL-3187 reset ViewStyle on Cancel in FeatureSettings

Options
    • -0
    • +6
    /src/jalview/gui/FeatureSettings.java
    • -0
    • +3
    /src/jalview/viewmodel/styles/ViewStyle.java
Sunday 17 Feb
6:19 pm

Ben Soares

JAL-3141 User warning when deleting old backup files that are newer than the previous backup file

Options
    • -1
    • +1
    /resources/lang/Messages.properties
    • -1
    • +1
    /resources/lang/Messages_es.properties
    • -1
    • +1
    /src/jalview/io/BackupFiles.java
Friday 15 Feb
7:38 pm

Ben Soares

JAL-3141 re-order deletion of old files and check lastModified times with their replacements

Options
    • -2
    • +6
    /resources/lang/Messages.properties
    • -2
    • +6
    /resources/lang/Messages_es.properties
    • -57
    • +259
    /src/jalview/io/BackupFiles.java
    • -20
    • +19
    /src/jalview/jbgui/GPreferences.java
7:45 am

Mungo Carstairs

Merge branch 'features/JAL-3010ontologyFeatureSettings' into merge/JAL-3187_JAL-3010

Options
    • -3
    • +12
    /src/jalview/gui/FeatureSettings.java
7:43 am

Mungo Carstairs

JAL-3010 getColumnClass() never return null

Options
    • -3
    • +12
    /src/jalview/gui/FeatureSettings.java
7:43 am

Mungo Carstairs

JAL-3010 getColumnClass() never return null

Options
    • -3
    • +12
    /src/jalview/gui/FeatureSettings.java
Thursday 14 Feb
3:52 pm

Ben Soares

JAL-3141 Added warning/confirmation when suffixReverse is changed without changing suffixTemplate or suffixDigits (Bad Things might happen to previous backup files)

Options
    • -1
    • +3
    /resources/lang/Messages.properties
    • -2
    • +4
    /resources/lang/Messages_es.properties
    • -4
    • +2
    /src/jalview/io/BackupFiles.java
    • -21
    • +53
    /src/jalview/jbgui/GPreferences.java
2:20 pm

Ben Soares

JAL-3141 Moved 'Previously saved scheme' combo box preference out to 'Cancel changes' button. Tidied up the Summary box display.

Options
    • -1
    • +2
    /resources/lang/Messages.properties
    • -1
    • +2
    /resources/lang/Messages_es.properties
    • -70
    • +103
    /src/jalview/jbgui/GPreferences.java
Wednesday 13 Feb
2:36 pm

Mungo Carstairs

JAL-3187 'on top' optional for complementary features

Options
    • -0
    • +4
    /src/jalview/api/ViewStyleI.java
    • -1
    • +21
    /src/jalview/gui/FeatureSettings.java
    • -39
    • +90
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
    • -0
    • +12
    /src/jalview/viewmodel/AlignmentViewport.java
    • -0
    • +14
    /src/jalview/viewmodel/styles/ViewStyle.java
2:36 pm

Mungo Carstairs

JAL-3187 'on top' optional for complementary features

Conflicts:

src/jalview/gui/FeatureSettings.java

Options
    • -0
    • +4
    /src/jalview/api/ViewStyleI.java
    • -6
    • +27
    /src/jalview/gui/FeatureSettings.java
    • -39
    • +90
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
    • -0
    • +12
    /src/jalview/viewmodel/AlignmentViewport.java
    • -0
    • +14
    /src/jalview/viewmodel/styles/ViewStyle.java
Tuesday 12 Feb
4:46 pm

Ben Soares

JAL-3196 Changes install4jHomeDir depending on Mac or Linux *needs improvingadd build.gradle

Options
    • -2
    • +8
    /gradle/jalview/build.gradle
11:28 am

Mungo Carstairs

Merge branch 'features/JAL-3010ontologyFeatureSettings' into merge/JAL-3187_JAL-3010

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/gui/FeatureSettings.java

src/jalview/gui/FeatureTypeSettings.java

Options
    • -0
    • +5
    /resources/lang/Messages.properties
    • -1
    • +6
    /resources/lang/Messages_es.properties
    • -7
    • +8
    /src/jalview/gui/AlignFrame.java
    • -1
    • +1
    /src/jalview/gui/CrossRefAction.java
    • -168
    • +391
    /src/jalview/gui/FeatureSettings.java
    • -22
    • +180
    /src/jalview/gui/FeatureTypeSettings.java
    • -33
    • +66
    /test/jalview/gui/AlignFrameTest.java
10:37 am

Mungo Carstairs

JAL-3032 default Autosearch to off for JalviewJS

Options
    • -2
    • +4
    /src/jalview/fts/core/GFTSPanel.java
8:44 am

Mungo Carstairs

JAL-3195 revised SequenceIdMatcher (tests todo)

Options
    • -19
    • +57
    /src/jalview/analysis/SequenceIdMatcher.java
    • -1
    • +1
    /src/jalview/io/FeaturesFile.java
Monday 11 Feb
7:56 pm

Ben Soares

JAL-3196 install4j media builder in gradle

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    • +41
    /gradle/jalview/build.gradle
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    • +1429
    /gradle/jalview/jalview.install4j
    • binary
    /resources/images/jetset_jalview_splash.gif
    • -0
    • +103
    /src/jalview/bin/Launcher.java
Friday 08 Feb
3:53 pm

Ben Soares

JAL-3194 new launcher, use like: java -cp classes:lib/* jalview.bin.Launcher -maxMem

Options
    • -0
    • +103
    /src/jalview/bin/Launcher.java
11:12 am

Ben Soares

JAL-3179 pre-install4j config

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    • +46
    /gradle/jalview/build.gradle
    • -4
    • +4
    /gradle/jalview/gradle.properties
Thursday 07 Feb
11:41 am

Mungo Carstairs

JAL-3140 updated to latest intervalstore.jar

Options
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    • +1
    /.classpath
    • binary
    /lib/intervalstore-v0.2.jar
    • binary
    /lib/intervalstore-v0.3.jar
Wednesday 06 Feb
3:27 pm

Mungo Carstairs

JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

Options
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    • +7
    /schemas/vamsas.xsd
    • -1
    • +1
    /src/jalview/analysis/AlignmentUtils.java
    • -19
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    /src/jalview/datamodel/DBRefEntry.java
    • -1
    • +1
    /src/jalview/datamodel/GeneLociI.java
    • -0
    • +91
    /src/jalview/datamodel/GeneLocus.java
    • -31
    • +4
    /src/jalview/datamodel/Sequence.java
    • -4
    • +5
    /src/jalview/ext/ensembl/EnsemblGene.java
    • -28
    • +6
    /src/jalview/ext/ensembl/EnsemblLookup.java
    • -28
    • +5
    /src/jalview/ext/ensembl/EnsemblMap.java
    • -4
    • +4
    /src/jalview/gui/CrossRefAction.java
    • -2
    • +3
    /src/jalview/io/SequenceAnnotationReport.java
    • -1
    • +1
    /src/jalview/io/vcf/VCFLoader.java
    • -8
    • +34
    /src/jalview/project/Jalview2XML.java
    • -1
    • +33
    /src/jalview/xml/binding/jalview/Sequence.java
    • -2
    • +2
    /test/jalview/analysis/AlignmentUtilsTests.java
    • -0
    • +83
    /test/jalview/project/Jalview2xmlTests.java
Tuesday 05 Feb
4:20 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

latest transpiler and runtime

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    /swingjs/SwingJS-site.zip
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    /swingjs/net.sf.j2s.core.jar
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    /swingjs/timestamp
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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
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    /swingjs/ver/3.2.4/timestamp
2:31 pm

Mungo Carstairs

JAL-3032 check enough sequences selected on construction

Options
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    • +1
    /src/jalview/gui/CalculationChooser.java
1:51 pm

Mungo Carstairs

Test (passes!) for dialog message truncation

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    • +30
    /utils/test/JalviewJSTest.java
1:36 pm

Mungo Carstairs

JAL-3048 JS-compatible confirm dialog on delete all

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    /src/jalview/gui/AlignFrame.java
    • -2
    • +2
    /src/jalview/gui/PopupMenu.java
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    • +6
    /src/jalview/jbgui/GAlignFrame.java
Monday 04 Feb
5:17 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JSON parsing from a StringInputStream

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    /swingjs/SwingJS-site.zip
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    /swingjs/timestamp
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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/timestamp