jalview

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

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Monday 11 Mar 2019
2:54 pm

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

JAL-3201 restore group colours correctly from project

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    • -4
    • +5
    /src/jalview/project/Jalview2XML.java
    • -1
    • +2
    /src/jalview/viewmodel/AlignmentViewport.java
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    • +1
    /test/jalview/project/Jalview2xmlTests.java
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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    • -1
    • +10
    /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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    • -2
    • +5
    /src/jalview/gui/SeqPanel.java
    • -1
    • +1
    /src/jalview/viewmodel/AlignmentViewport.java
    • -4
    • +29
    /test/jalview/gui/AlignViewportTest.java
Monday 25 Feb 2019
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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    • +10
    /test/jalview/schemes/ResiduePropertiesTest.java
Sunday 24 Feb 2019
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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    • -2
    • +2
    /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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    • -1
    • +13
    /src/jalview/datamodel/SequenceGroup.java
    • -6
    • +2
    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/ScalePanel.java
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    • +36
    /test/jalview/datamodel/SequenceGroupTest.java
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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    • -1
    • +1
    /src/jalview/gui/AlignFrame.java
    • -11
    • +7
    /src/jalview/gui/AlignmentPanel.java
    • -1
    • +1
    /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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    • +64
    /test/jalview/io/vcf/VCFLoaderTest.java
Thursday 24 Jan 2019
2:30 pm

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

JAL-3018 Ensembl version updated to 9.0

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    • +3
    /src/jalview/ext/ensembl/EnsemblRestClient.java
Wednesday 23 Jan 2019
9:15 am

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

JAL-3063 correct handling of absent choice element in DBRef Mapping

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    • -6
    • +7
    /src/jalview/project/Jalview2XML.java
Thursday 17 Jan 2019
12:29 pm

Jim Procter

JAL-3116 clear out whitespace when materialising Sequence object from Uniprot XML

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    • -8
    • +4
    /src/jalview/ws/dbsources/Uniprot.java
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    • +2
    /test/jalview/ws/dbsources/UniprotTest.java
Wednesday 16 Jan 2019
11:38 am

Jim Procter

Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop

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    • +1
    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
    • -19
    • +44
    /src/jalview/gui/FeatureSettings.java
Tuesday 15 Jan 2019
1:12 pm

Jim Procter

JAL-1767 test that changing view association for PCA panel can be restored

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    • -2
    • +5
    /test/jalview/project/Jalview2xmlTests.java
1:10 pm

Jim Procter

JAL-1767 refactor associated view logic to public method and synchronise PCAPanel.av/ap with RotateableCanvac.ap/av

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    • -5
    • +18
    /src/jalview/gui/PCAPanel.java
11:19 am

Jim Procter

JAL-1767 patch buggy PCA view association test

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    • -1
    • +8
    /test/jalview/project/Jalview2xmlTests.java
Monday 14 Jan 2019
4:13 pm

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

JAL-3186 remove Variable Colour from popup menu

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    • +2
    /resources/lang/Messages.properties
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    • +2
    /resources/lang/Messages_es.properties
    • -66
    • +3
    /src/jalview/gui/FeatureSettings.java
4:00 pm

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

JAL-3186 remove duplicate message keys

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    • +0
    /resources/lang/Messages.properties
    • -1
    • +0
    /resources/lang/Messages_es.properties
2:25 pm

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

JAL-2069 clear any error colour when setting threshold from slider

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    • -0
    • +1
    /src/jalview/gui/FeatureTypeSettings.java
Wednesday 09 Jan 2019
5:29 pm

Jim Procter

JAL-1767 failing test to check if the PCA view association is correctly saved and restored

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    • -0
    • +56
    /test/jalview/project/Jalview2xmlTests.java
4:24 pm

Jim Procter

Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767

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4:23 pm

Jim Procter

JAL-3063 remove stale JAXB binding POJO

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    • -5090
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    /src/jalview/xml/binding/jalview/JalviewModelType.java
4:22 pm

Jim Procter

Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767

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4:16 pm

Jim Procter

JAL-3063 - ant task for regenerating JAXB schema - could be optimised further

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    /.ant-targets-build.xml
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    • +44
    /build.xml
Thursday 03 Jan 2019
10:28 am

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

JAL-1889 additional test for clover-added fields

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    • -0
    • +4
    /test/jalview/viewmodel/styles/ViewStyleTest.java
9:16 am

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

JAL-1889 ignore 'synthetic' fields added for jacoco

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    • +10
    /test/jalview/viewmodel/styles/ViewStyleTest.java
Friday 21 Dec 2018
11:48 am

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

JAL-1767 minimise local variable scope

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    • -7
    • +5
    /src/jalview/project/Jalview2XML.java
Thursday 20 Dec 2018
1:36 pm

Jim Procter

JAL-1767 port save/load PCA panel to JAXB - JAL-3063

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    /src/jalview/gui/Jalview2XML.java
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    • +87
    /src/jalview/gui/PCAPanel.java
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    /src/jalview/gui/RotatableCanvas.java
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    /src/jalview/gui/TreeCanvas.java
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    • +360
    /src/jalview/project/Jalview2XML.java
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    /src/jalview/xml/binding/jalview/AlcodonFrame.java
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    /src/jalview/xml/binding/jalview/Annotation.java
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    /src/jalview/xml/binding/jalview/AnnotationColourScheme.java
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    /src/jalview/xml/binding/jalview/AnnotationElement.java
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    /src/jalview/xml/binding/jalview/DoubleMatrix.java
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    /src/jalview/xml/binding/jalview/DoubleVector.java
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    /src/jalview/xml/binding/jalview/Feature.java
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    /src/jalview/xml/binding/jalview/FeatureMatcher.java
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    /src/jalview/xml/binding/jalview/FeatureMatcherSet.java
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    /src/jalview/xml/binding/jalview/FilterBy.java
  16. … 15 more files in changeset.
11:46 am

Jim Procter

JAL-3171 JAL-3063 merge updates from JAL-1767

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    /src/jalview/gui/Jalview2XML.java
Wednesday 19 Dec 2018
4:53 pm

Jim Procter

Merge branch 'features/JAL-1767pcaInProject' into bug/JAL-3171_maintain_datasets_across_views

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /schemas/jalview.xsd
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/Jalview2XML.java
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    /src/jalview/gui/PCAPanel.java
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    /src/jalview/gui/TreePanel.java
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    /test/jalview/io/Jalview2xmlTests.java
11:38 am

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

JAL-2791 JAL-2808 correct Javadoc for api method

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    /src/jalview/api/FeatureRenderer.java