jalview

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JAL-2909 Changes to htsjdk import control

JAL-2909 Cigar parsing tests

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    /test/jalview/datamodel/CigarParserTest.java
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

JAL-984 remove all references to idwidth.gif - in build.xml too :)

JAL-2885 release notes

JAL-2599 corrected case-insensitive symbol indexing

Merge branch 'features/JAL-2885UniprotHttps' into releases/Release_2_10_4_Branch

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    /src/jalview/ext/ensembl/EnsemblLookup.java
JAL-2599 parser and datamodel use primitive double[] not List<Double>

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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/datamodel/HMMNode.java
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    /src/jalview/datamodel/HiddenMarkovModel.java
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    /src/jalview/io/HMMFile.java
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    /test/jalview/io/HMMFileTest.java
JAL-2885 xfam https

JAL-2885 XFAM_DOMAIN->XFAM_BASEURL

JAL-2885 Ensembl* -> https

JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL

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    /src/jalview/ext/ensembl/EnsemblGenomes.java
JAL-2885 renamed base URL getter from getDomain..

JAL-2629 tidy tests, refactor hmmer node mapping slightly

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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/hmmer/HMMAlignThread.java
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    /src/jalview/hmmer/HMMBuildThread.java
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    /test/jalview/hmmer/HMMERTest.java
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    /test/jalview/hmmer/testProps.jvprops
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    /test/jalview/io/HMMFileTest.java
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

JAL-984 ID width adjuster needs to be white !

JAL-2666 release notes

Merge branch 'bug/JAL-2666' into releases/Release_2_10_4_Branch

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    /src/jalview/gui/AlignmentPanel.java
Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

JAL-984 remove all references to idwidth.gif and use int constants in place of width/height of image when switching between margin adjustment active/inactive mouse cursor

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    • +9
    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/IdwidthAdjuster.java
JAL-2906 typo fixes

JAL-984 release notes

Merge branch 'feature/JAL-984splitAdjuster' into releases/Release_2_10_4_Branch

JAL-294 remove unneeded paint() method

JAL-984 remove commented/unnecessary if clause

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    /src/jalview/gui/AnnotationLabels.java
JAL-2629 tidy unit tests, constants etc

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    • +72
    /src/jalview/analysis/AAFrequency.java
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    • +9
    /src/jalview/datamodel/SequenceGroup.java
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    /src/jalview/gui/AnnotationLabels.java
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    /test/jalview/datamodel/HiddenMarkovModelTest.java
JAL-2906 release notes for 2.10.4

Merge branch 'bug/JAL-2778again' into releases/Release_2_10_4_Branch

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    /src/jalview/datamodel/Alignment.java
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    • +8
    /src/jalview/gui/AnnotationPanel.java
JAL-2778 reinstate transparent windows to avoid ugly borders on OSX

JAL-2629 simplifying method signatures in Hmmer command classes

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    /src/jalview/hmmer/HMMAlignThread.java
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    • +158
    /src/jalview/hmmer/HMMBuildThread.java
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    /src/jalview/hmmer/HMMERParamStore.java
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    /src/jalview/hmmer/HMMSearchThread.java
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    /src/jalview/hmmer/HmmerCommand.java