jalview

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Commits this week: 2
Total Committers: 72
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Commits this week: 2

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Wednesday 27 Feb 2019
1:53 pm

Ben Soares

JAL-3196 tidying for demo

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    /getdown/getdown-core-1.8.3-SNAPSHOT.jar
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    /gradle/jalview/build.gradle
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    /gradle/jalview/jalview_getdown.install4j
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12:31 pm

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

JAL-3202 discard zero percentages in extracted profile

Conflicts:

src/jalview/renderer/AnnotationRenderer.java

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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/renderer/AnnotationRenderer.java
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    /test/jalview/analysis/AAFrequencyTest.java
12:31 pm

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

JAL-3202 discard zero percentages in extracted profile

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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/renderer/AnnotationRenderer.java
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    /test/jalview/analysis/AAFrequencyTest.java
9:15 am

Ben Soares

JAL-3196 deleting old file

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    /gradle/jalview/OLD_build.gradle
3:11 am

Ben Soares

JAL-3196 fixed getdown progress bar position

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    /gradle/jalview/gradle.properties
2:54 am

Ben Soares

JAL-3196 Substantial addition of getdown automation in getdown, and new getdown-based launchers packaged by install4j

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    /.gitignore
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    /getdown/files/getdown.txt
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    /gradle/jalview/build.gradle
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    /gradle/jalview/jalview_getdown.install4j
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Tuesday 26 Feb 2019
11:39 am

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

JAL-3201 JAL-2386 don't pre-select 'apply to all groups'

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    /src/jalview/gui/SliderPanel.java
10:41 am

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

JAL-3201 group colour schemes distinct instances

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    /src/jalview/gui/SeqPanel.java
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    /src/jalview/viewmodel/AlignmentViewport.java
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    /test/jalview/gui/AlignViewportTest.java
Monday 25 Feb 2019
7:32 pm

Ben Soares

JAL-3196 new background image

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    /resources/images/jalview_logo_background_fade-640x480.png
3:54 pm

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

JAL-3032 Jalview (as JS) parse query params to main arguments

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    /src/jalview/bin/Jalview.java
3:24 pm

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

JAL-3032 JalviewJS2 converts url query parameters to 'applet' args

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    /src/jalview/bin/JalviewJS2.java
1:46 pm

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

JAL-3200 fast lookup of DSSP3 notation

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    /src/jalview/schemes/ResidueProperties.java
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    /test/jalview/schemes/ResiduePropertiesTest.java
Sunday 24 Feb 2019
7:58 pm

Ben Soares

JAL-3196 some changes

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    /getdown/files/getdown.txt
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    /gradle/jalview/build.gradle
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    /gradle/jalview/gradle.properties
8:58 am

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

JAL-3198 don't recalculate group conservation for Id Panel selection

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    /src/jalview/gui/IdPanel.java
8:10 am

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

JAL-3198 SequenceGroup 'bulk constructor' without duplicates check

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    /src/jalview/datamodel/SequenceGroup.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/ScalePanel.java
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    /test/jalview/datamodel/SequenceGroupTest.java
Saturday 23 Feb 2019
12:36 pm

Ben Soares

JAL-3196 Initial addition of getdown

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    /getdown/files/getdown.txt
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    /getdown/getdown-core-1.8.3-SNAPSHOT.jar
12:20 pm

Ben Soares

JAL-3196 changed test Launcher to default to maxMem

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    /src/jalview/bin/Launcher.java
12:18 pm

Ben Soares

JAL-3196 extra output file used for gradle incremental builds

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    /.gitignore
12:14 pm

Ben Soares

JAL-3196 updates to install4j config

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    /gradle/jalview/build.gradle
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Friday 22 Feb 2019
11:27 am

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

JAL-2915 don't recalculate Overview on scroll to position, ever!

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/SeqPanel.java
10:04 am

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

JAL-2738 don't set AF as feature score

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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
9:19 am

Ben Soares

JAL-3141 improved message for asking whether to delete files (file modification time and size added to info to help user decide

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    /resources/lang/Messages.properties
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    /src/jalview/io/BackupFiles.java
Thursday 21 Feb 2019
5:59 pm

Ben Soares

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

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    /src/jalview/io/BackupFiles.java
2:49 pm

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

JAL-3187 handle no mapping / complement features without NPE

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    /src/jalview/datamodel/MappedFeatures.java
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    /src/jalview/gui/SeqPanel.java
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    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
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    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
Wednesday 20 Feb 2019
4:40 pm

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

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

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
12:15 pm

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

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

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    /src/jalview/datamodel/MappedFeatures.java
Tuesday 19 Feb 2019
12:01 pm

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

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

Conflicts:

src/jalview/gui/FeatureSettings.java

src/jalview/renderer/seqfeatures/FeatureRenderer.java

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    /src/jalview/gui/FeatureSettings.java
11:15 am

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

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

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    /src/jalview/datamodel/MappedFeatures.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/SeqPanel.java
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    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
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    /src/jalview/structure/SequenceListener.java
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    /src/jalview/structure/StructureSelectionManager.java
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    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
Monday 18 Feb 2019
9:19 am

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

JAL-3187 reset ViewStyle on Cancel in FeatureSettings

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    /src/jalview/gui/FeatureSettings.java
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    /src/jalview/viewmodel/styles/ViewStyle.java
Sunday 17 Feb 2019
6:19 pm

Ben Soares

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

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