jalview

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JAL-914 singleton HelpBroker to avoid multiple help windows

JAL-2754 reinstate PA import from bad conflict merge

JAL-2754 remove duplicate classpath entry again

Merge branch 'releases/Release_2_10_4_Branch' into develop

Merge branch 'patch/JAL-2754_patch2104forJava8' into releases/Release_2_10_4_Branch

JAL-2754 don’t use deprecated api for getting font metrics

JAL-2754 fix eclipse compilation error about referencing deprecated API via @see

JAL-2929 use configure Overview gap colour instead of white past end of sequence

Merge branch 'patch/JAL-2754_patch2104forJava8' into develop

Merge branch 'patch/JAL-2754_patch2104forJava8' into releases/Release_2_10_4_Branch

JAL-2754 dont put '<>' in <echo> text!

Merge branch 'releases/Release_2_10_4_Branch' into develop

Merge branch 'patch/JAL-2754_patch2104forJava8' into releases/Release_2_10_4_Branch

JAL-2754 clean up proguard path spec and config variables

JAL-2679 getGeneId() now uses the same pattern as getGeneLoci, getSpecies

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    • +17
    /src/jalview/ext/ensembl/EnsemblLookup.java
Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into develop

Conflicts:

src/jalview/ext/ensembl/EnsemblLookup.java

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    • +0
    /src/jalview/ext/ensembl/EnsemblLookup.java
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    • +22
    /test/jalview/io/CrossRef2xmlTests.java
JAL-2922 update FeatureRenderer and repaint feature settings after Invert Selection

Merge branch 'bug/JAL-2865removeGC' into develop

JAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES

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    /src/jalview/ext/ensembl/EnsemblGenomes.java
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    /test/jalview/analysis/CrossRefTest.java
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    /test/jalview/io/CrossRef2xmlTests.java
JAL-2893 include ENSEMBLGENOMES as a 'roundtrip db source'

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    /src/jalview/datamodel/DBRefSource.java
JAL-2679 reinstating changes lost in VCF merge

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    /src/jalview/ext/ensembl/EnsemblLookup.java
JAL-2679 reinstating changes lost in VCF merge

Conflicts:

src/jalview/ext/ensembl/EnsemblLookup.java

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    /src/jalview/ext/ensembl/EnsemblLookup.java
JAL-2913 use FIGURE_FIXEDIDWIDTH (not FIGURE_USERIDWIDTH)

Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into merges/JAL-2906_update2_11_from_2_10_4

JAL-2885 tests updated for code changes

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    /test/jalview/ws/dbsources/PfamFullTest.java
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    /test/jalview/ws/dbsources/PfamSeedTest.java
    • -3
    • +5
    /test/jalview/ws/dbsources/RfamFullTest.java
    • -5
    • +5
    /test/jalview/ws/dbsources/RfamSeedTest.java
JAL-2930 use MouseWheelEvent.getPreciseWheelRotation, not getWheelRotation

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    /src/jalview/gui/RotatableCanvas.java
Merge branch 'releases/Release_2_10_4_Branch' into develop check carefully that JAL-2885 (configurable Ensembl/Genomes Endpoints) functionality is still present

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    /src/jalview/analysis/AlignmentUtils.java
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    • +11
    /src/jalview/appletgui/AlignFrame.java
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    • +97
    /src/jalview/datamodel/Sequence.java
    • -0
    • +30
    /src/jalview/datamodel/SequenceI.java
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    /src/jalview/ext/ensembl/EnsemblInfo.java
    • -0
    • +22
    /src/jalview/ext/ensembl/EnsemblLookup.java
    • -28
    • +12
    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AnnotationLabels.java
  1. … 7 more files in changeset.
Merge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch

JAL-2922 [2] not [1] for Boolean column of table