jalview

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Tuesday 16 May 2017
4:10 pm

Kira Mourão

JAL-2536 Overview window sizing not subject to min size restrictions

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    • -1
    • +1
    /src/jalview/gui/AlignFrame.java
    • -6
    • +11
    /src/jalview/gui/Desktop.java
1:40 pm

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

JAL-2403 simplify instantiation / configuration of score model for view

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    • -4
    • +19
    /src/jalview/analysis/scoremodels/FeatureDistanceModel.java
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    • +10
    /src/jalview/analysis/scoremodels/PIDModel.java
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    • +10
    /src/jalview/analysis/scoremodels/ScoreMatrix.java
    • -15
    • +1
    /src/jalview/analysis/scoremodels/ScoreModels.java
    • -0
    • +8
    /src/jalview/analysis/scoremodels/SmithWatermanModel.java
    • -0
    • +11
    /src/jalview/api/analysis/ScoreModelI.java
    • -37
    • +0
    /src/jalview/api/analysis/ViewBasedAnalysisI.java
11:34 am

Kira Mourão

JAL-2522 Missed fix to applet

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    • -1
    • +1
    /src/jalview/appletgui/SeqPanel.java
10:37 am

Kira Mourão

JAL-2388 Rationalised hashCode method in HiddenColumns

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    • -2
    • +3
    /src/jalview/datamodel/HiddenColumns.java
9:48 am

Jim Procter

Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

Options
Monday 15 May 2017
7:23 pm

Jim Procter

JAL-2507 fix test: knockon from capitalisation on secondary structure from stockholm file

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    • -1
    • +1
    /test/jalview/datamodel/AlignmentTest.java
5:37 pm

Jim Procter

Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

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    • -1
    • +2
    /test/jalview/io/AnnotationFileIOTest.java
5:37 pm

Jim Procter

JAL-2311 disable and relocate Jared service tests to Network (prior to their removal)

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    • -4
    • +5
    /test/jalview/ws/jabaws/JpredJabaStructExportImport.java
5:26 pm

Jim Procter

JAL-2507 capitalisation for annotation lines generated from stockholm annotation

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    • -4
    • +4
    /src/jalview/io/StockholmFile.java
4:56 pm

Jim Procter

JAL-2507 case insensitive recognition of annotation type

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    • -2
    • +2
    /src/jalview/io/StockholmFile.java
4:43 pm

Jim Procter

JAL-2507 - required callers to specify exact ignore flags for StockholmFileTest.testAlignmentEquivalent asserts

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    • -1
    • +2
    /test/jalview/io/AnnotationFileIOTest.java
    • -1
    • +2
    /test/jalview/io/PhylipFileTests.java
    • -1
    • +1
    /test/jalview/io/RNAMLfileTest.java
    • -4
    • +8
    /test/jalview/io/StockholmFileTest.java
    • -1
    • +2
    /test/jalview/ws/jabaws/DisorderAnnotExportImport.java
    • -1
    • +2
    /test/jalview/ws/jabaws/JpredJabaStructExportImport.java
    • -1
    • +2
    /test/jalview/ws/jabaws/RNAStructExportImport.java
4:26 pm

Jim Procter

JAL-2535 quick hack to implement posterior probabilities parsing. 0-9 parsed as 0..9, ‘*’ or any other non-whitespace symbol parsed as ’10’.

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    • -1
    • +25
    /src/jalview/io/StockholmFile.java
3:50 pm

Kira Mourão

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

Options
3:50 pm

Kira Mourão

JAL-2388 Add missed optimisation

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    • -10
    • +17
    /src/jalview/renderer/OverviewRenderer.java
12:14 pm

Jim Procter

Merge branch 'features/JAL-2376_add-horizontal-bar' into develop

Options
12:07 pm

Jim Procter

JAL-2371 create a default ResidueShader when constructing the viewport

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    • -1
    • +1
    /src/jalview/viewmodel/AlignmentViewport.java
Friday 12 May 2017
3:48 pm

Jim Procter

Merge branch 'features/JAL-2435splitScreenFont' into develop

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    • -0
    • +1
    /help/help.jhm
    • -1
    • +2
    /help/helpTOC.xml
    • -0
    • +1
    /resources/lang/Messages.properties
    • -1
    • +2
    /resources/lang/Messages_es.properties
    • -6
    • +14
    /src/jalview/appletgui/AlignViewport.java
    • -2
    • +2
    /src/jalview/appletgui/AlignmentPanel.java
    • -1
    • +3
    /src/jalview/appletgui/SeqPanel.java
    • -8
    • +5
    /src/jalview/gui/AlignViewport.java
    • -13
    • +51
    /src/jalview/gui/SeqPanel.java
    • -0
    • +12
    /src/jalview/viewmodel/AlignmentViewport.java
3:47 pm

Jim Procter

JAL-2418 broken help ref

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    • +1
    /help/helpTOC.xml
3:46 pm

Jim Procter

JAL-2435 documentation and what’s new

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    • -0
    • +1
    /help/help.jhm
    • -0
    • +1
    /help/helpTOC.xml
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    • +3
    /help/html/features/splitView.html
3:42 pm

Jim Procter

JAL-2435 mention new checkbox in linked cDNA/Protein view documentation

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    • -1
    • +4
    /help/html/features/splitView.html
3:41 pm

Jim Procter

JAL-2435 mirror antiAlias setting between cDNA and Protein

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    • -1
    • +16
    /src/jalview/gui/FontChooser.java
3:09 pm

Jim Procter

Merge branch 'features/JAL-2388OverviewWindow' into develop

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    • +2
    /help/help.jhm
    • -0
    • +1
    /help/helpTOC.xml
    • -1
    • +2
    /resources/lang/Messages.properties
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    • +1
    /resources/lang/Messages_es.properties
    • -13
    • +17
    /src/jalview/gui/AlignFrame.java
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    • +34
    /src/jalview/gui/SeqPanel.java
    • -3
    • +4
    /src/jalview/gui/SequenceRenderer.java
3:01 pm

Jim Procter

JAL-2388 mention overview popup in documentation

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    • +2
    /help/help.jhm
    • -0
    • +1
    /help/helpTOC.xml
    • -0
    • +5
    /help/html/features/overview.html
2:56 pm

Jim Procter

JAL-2388 checkbox in overview popup for applet

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    • -8
    • +8
    /src/jalview/appletgui/OverviewPanel.java
2:29 pm

Jim Procter

Merge branch 'features/JAL-2228_efficient_featurecounts' into develop

Options
2:29 pm

Jim Procter

JAL-2228 updated script in help docs, renamed docs, and added note about non-backwards compatibility of feature counter script

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    • +25
    /examples/groovy/featuresCounter.groovy
    • -1
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    /help/help.jhm
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    /help/helpTOC.xml
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    /help/html/features/groovy.html
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    /help/html/groovy/featureCounter.html
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    • +123
    /help/html/groovy/featuresCounter.html
Thursday 11 May 2017
4:21 pm

Jim Procter

Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

Options
4:20 pm

Jim Procter

JAL-2509 JAL-2507 allow whitespace in GS annotation lines (removed old code for processing GS column annotation into features)

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    • -22
    • +30
    /src/jalview/io/StockholmFile.java
4:17 pm

Jim Procter

JAL-2507 JAL-2509 allow whitespace==null for annotation row comparison, and test coverage for Annotation equivalence asserts

Options
    • -20
    • +165
    /test/jalview/io/StockholmFileTest.java
3:29 pm

Jim Procter

JAL-2507 test if an annotation is ‘whitespace’

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    • -0
    • +14
    /src/jalview/datamodel/Annotation.java