jalview

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JAL-2136 New Phyre2 branch + attempt to resynced with develop

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/io/AnnotationFile.java
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JAL-2577 mirror select/hide by annotation in split frame applet, and on Cancel

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    /src/jalview/gui/AnnotationColumnChooser.java
JAL-2577 mirror hide/select columns by annotation across split frame

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    /src/jalview/gui/AnnotationColumnChooser.java
JAL-2418 updated release branch/version and release date before forking release branch

Merge branch 'bug/JAL-2586' into develop

JAL-2586 Clarification to URL link code

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    /test/jalview/urls/UrlLinkDisplayTest.java
Merge branch 'documentation/JAL-2418_release2102' into develop

JAL-2590 release notes

Merge branch 'bug/JAL-2590' into develop

JAL-2590 patch for rendering eggnog trees with polytomies (also see

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    /src/jalview/appletgui/TreeCanvas.java
Merge branch 'documentation/JAL-2418_release2102' into develop

JAL-2576 release notes

Merge branch 'bug/JAL-2576' into develop

Merge branch 'bug/JAL-2586' into develop

JAL-2136 Introduced DynamicData model, modified AnnotionFile to store Phyre meta-data in DynamicData object, modified SequenceAnnotationReport to build Phyre html meta-data from DynamicData list

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    /src/jalview/datamodel/DynamicData.java
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    /src/jalview/io/AnnotationFile.java
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    /src/jalview/io/AnnotationUtil.java
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    /test/jalview/io/AnnotationFileIOTest.java
JAL-2586 Checkstyle flagged fix of unintended fall through

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    /src/jalview/urls/UrlLinkDisplay.java
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    /test/jalview/urls/UrlLinkDisplayTest.java
Merge branch 'spikes/phyre' into features/JAL-2136_phyre2_integration

JAL-2571 Missed (alwaysRun=true) for @BeforeMethod

JAL-2228 java 1.7 compliance

JAL-2291 updated docs

JAL-2291 only hide/show columns intersecting with currently selected region.

JAL-2291 get bitset representing hidden columns

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2291 use HiddenColumns.hideMarkedBits and take union of selection and sequence under popup

JAL-2291 method taking a BitSet for hiding columns

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2291 bug fix - BitSet.set is [start,end+1)

JAL-2291 fixed broken asserts for SequenceI.getInsertionsAsBits

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    /test/jalview/datamodel/SequenceTest.java
JAL-2291 ‘Hide Insertions’ now operates on selection or if none available, the sequence that was right-clicked on.

JAL-2291 SequenceI.getInsertionsAsBits for convenient logical operations

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    /src/jalview/datamodel/Sequence.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-2582 comment about IDs being lost if they resembl ensembl IDs but can’t be resolved to a genomic ID.

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    /src/jalview/ext/ensembl/EnsemblGene.java
JAL-2582 recognise ENS…P peptide IDs and make two getParent requests to get gene ID.

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    /src/jalview/ext/ensembl/EnsemblGene.java