jalview

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Friday 01 Nov 2019
3:21 pm

Ben Soares

JAL-3474 removed all .cvsignore files stored in the repo

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    /.cvsignore
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    /dist/.cvsignore
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    /help/help/html/.cvsignore
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    /help/help/html/colourSchemes/.cvsignore
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    /help/help/html/editing/.cvsignore
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    /help/help/html/features/.cvsignore
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    /help/help/html/io/.cvsignore
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    /help/help/html/misc/.cvsignore
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    /help/help/html/webServices/.cvsignore
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    /resources/.cvsignore
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    /resources/images/.cvsignore
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    /schemas/.cvsignore
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    /src/MCview/.cvsignore
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    /src/jalview/.cvsignore
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    /src/jalview/analysis/.cvsignore
  16. … 8 more files in changeset.
Tuesday 15 Oct 2019
4:11 pm

Jim Procter

JAL-3407 update release date for Jalview 2.11.1

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    /help/help/html/releases.html
Friday 11 Oct 2019
11:00 am

Jim Procter

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

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Thursday 26 Sep 2019
3:42 pm

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

JAL-2481 remove code duplication left by merge

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    /src/jalview/datamodel/Sequence.java
2:59 pm

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

JAL-3441 action double-click in Feature Type column only

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    /src/jalview/gui/FeatureSettings.java
Friday 23 Aug 2019
3:38 pm

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

JAL-3141 correct cast of spinner value

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    /src/jalview/jbgui/GPreferences.java
Thursday 22 Aug 2019
4:06 pm

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

JAL-3187 case-insensitive codon variant calculation

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    /src/jalview/datamodel/MappedFeatures.java
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    /test/jalview/datamodel/MappedFeaturesTest.java
Wednesday 21 Aug 2019
5:01 pm

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

JAL-3187 minor code tidying, todo removal

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    /src/jalview/datamodel/MappedFeatures.java
Monday 12 Aug 2019
4:35 pm

Jim Procter

JAL-2987 release notes

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    /help/help/html/releases.html
3:15 pm

Jim Procter

JAL-3407 update RELEASE and cut new release notes in releaseHistory.html

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    /RELEASE
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    /help/help/html/releases.html
2:54 pm

Jim Procter

JAL-3407 JAL-3406 update credits in Jalview 2.11.1

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    /help/help/html/index.html
Friday 09 Aug 2019
9:01 am

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

JAL-3187 removal of variant feature (non-virtual) transfer to protein

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/CrossRef.java
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    /test/jalview/analysis/AlignmentUtilsTests.java
Wednesday 07 Aug 2019
10:25 am

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

JAL-3187 (fudge) look in both alignments for stored mappings

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    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
9:42 am

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

Merge branch 'develop' into feature/JAL-3187linkedFeatures

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    /src/jalview/project/Jalview2XML.java
Wednesday 31 Jul 2019
12:59 pm

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

JAL-3389 add .py to restored Chimera session filename so it opens!

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    /src/jalview/project/Jalview2XML.java
9:10 am

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

Merge branch 'bug/JAL-3388structureChooserSorting' into develop

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Tuesday 30 Jul 2019
6:45 pm

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

JAL-3198 more efficient Sequence.getDisplayId()

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    /src/jalview/datamodel/Sequence.java
5:51 pm

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

JAL-3388 correct class for column 0 Ref Sequence

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    /src/jalview/fts/core/FTSRestResponse.java
Monday 29 Jul 2019
3:48 pm

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

JAL-3386 correct wrapped width calculation for headless image export

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    /src/jalview/gui/AlignmentPanel.java
3:35 pm

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

JAL-3377 more reused of SeqCanvas.computeWrappedGeometry

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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/IdCanvas.java
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    /src/jalview/gui/SeqCanvas.java
11:44 am

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

JAL-3377 add seq-annotations gap to cheight not to hgap

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    /src/jalview/gui/IdCanvas.java
11:34 am

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

JAL-3377 Javadoc added for getWrappedHeight()

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    /src/jalview/gui/AlignmentPanel.java
11:20 am

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

JAL-3377 include seq-annotation spacing in getWrappedHeight()

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    /src/jalview/gui/AlignmentPanel.java
Sunday 28 Jul 2019
11:05 am

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

JAL-3377 corrected wrapped widths height for IdCanvas

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    /src/jalview/gui/IdCanvas.java
Friday 26 Jul 2019
7:42 pm

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

Merge branch 'features/JAL-3375vcfValidation' into feature/JAL-3187linkedFeatures

Conflicts:

src/jalview/io/vcf/VCFLoader.java

test/jalview/io/vcf/VCFLoaderTest.java

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    /src/jalview/io/SequenceAnnotationReport.java
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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
5:52 pm

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

JAL-1793 only decode specific special characters in VCF data

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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
4:58 pm

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

JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature attributes

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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
2:40 pm

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

JAL-3375 format validate VCF Integer and Float fields

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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
Thursday 25 Jul 2019
11:48 am

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

JAL-3375 ignore '.' values for VCF data

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    /src/jalview/datamodel/features/FeatureAttributes.java
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    /src/jalview/io/vcf/VCFLoader.java
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    /test/jalview/io/vcf/VCFLoaderTest.java
Tuesday 16 Jul 2019
5:13 pm

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

Merge branch 'develop' into feature/JAL-3187linkedFeatures

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