jalview

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

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

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    /src/jalview/analysis/scoremodels/ScoreMatrix.java
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    /src/jalview/analysis/scoremodels/ScoreModels.java
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    /src/jalview/api/analysis/ScoreModelI.java
JAL-2522 Missed fix to applet

JAL-2388 Rationalised hashCode method in HiddenColumns

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    /src/jalview/datamodel/HiddenColumns.java
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

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

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

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    /test/jalview/io/AnnotationFileIOTest.java
JAL-2311 disable and relocate Jared service tests to Network (prior to their removal)

JAL-2507 capitalisation for annotation lines generated from stockholm annotation

JAL-2507 case insensitive recognition of annotation type

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

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    /test/jalview/io/AnnotationFileIOTest.java
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    /test/jalview/io/StockholmFileTest.java
JAL-2535 quick hack to implement posterior probabilities parsing. 0-9 parsed as 0..9, ‘*’ or any other non-whitespace symbol parsed as ’10’.

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

JAL-2388 Add missed optimisation

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

JAL-2371 create a default ResidueShader when constructing the viewport

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

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    /resources/lang/Messages_es.properties
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    /src/jalview/appletgui/AlignViewport.java
JAL-2418 broken help ref

JAL-2435 documentation and what’s new

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

JAL-2435 mirror antiAlias setting between cDNA and Protein

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

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/SequenceRenderer.java
JAL-2388 mention overview popup in documentation

JAL-2388 checkbox in overview popup for applet

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    /src/jalview/appletgui/OverviewPanel.java
Merge branch 'features/JAL-2228_efficient_featurecounts' into develop

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

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    /examples/groovy/featuresCounter.groovy
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    /help/html/groovy/featureCounter.html
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    /help/html/groovy/featuresCounter.html
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

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

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    /src/jalview/io/StockholmFile.java
JAL-2507 JAL-2509 allow whitespace==null for annotation row comparison, and test coverage for Annotation equivalence asserts

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    /test/jalview/io/StockholmFileTest.java
JAL-2507 test if an annotation is ‘whitespace’

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    /src/jalview/datamodel/Annotation.java