jalview

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JAL-3518 removed unneeded override in ChimeraCommands

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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
JAL-3518 removed unneeded override in ChimeraCommands

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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
JAL-3018 Ensembl reviewed REST version updated to 13.0

JAL-1191 use Cache.log for logging

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    /src/jalview/ext/so/SequenceOntology.java
JAL-3730 retry ping before failing; sysout logging changed to Cache.log

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    /src/jalview/ext/ensembl/EnsemblMap.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-3676 adding Axis and Castor loggging properties to the help text

JAL-3725 restrict mapped virtual feature location to mapped region Conflicts: src/jalview/gui/PopupMenu.java

JAL-3725 restrict mapped virtual feature location to mapped region

JAL-3725 restrict mapped virtual feature location to mapped region

JAL-3728 Icon and setting icon for Java Console

    • binary
    /resources/images/JalviewConsole.png
    • binary
    /utils/images/JalviewConsole_Huge.xcf
JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs

JAL-3725 helper methods for computing mapped feature range overlap

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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3725 helper methods for computing mapped feature range overlap

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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3725 helper methods for computing mapped feature range overlap

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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3725 exclude stop codon from CDS-to-protein mapping

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    /src/jalview/ws/dbsources/EmblXmlSource.java
JAL-3725 exclude stop codon from CDS-to-protein mapping

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    /src/jalview/ws/dbsources/EmblXmlSource.java
JAL-3725 exclude stop codon from CDS-to-protein mapping

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    /src/jalview/ws/dbsources/EmblXmlSource.java
Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch

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    /src/jalview/gui/AlignViewport.java
report JAL-3127 as known defect (fix targeted for 2.11.2)

JAL-3018 updated reviewed REST version to 12.0

Merge branch 'releases/Release_2_11_1_Branch' into feature/JAL-3719_gapColourInAlignmentView

JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam

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    /test/jalview/io/FileIOTester.java
JAL-3615 code tidy, improve unit test

JAL-2656 better read of (potential) gzip magic bytes

JAL-3719 patch test for user colour scheme with/out gap color

JAL-3719 patch test for user colour scheme with/out gap color

JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/SequenceRenderer.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /src/jalview/renderer/OverviewResColourFinder.java
JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer Conflicts: resources/lang/Messages.properties resources/lang/Messages_es.properties

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/SequenceRenderer.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /src/jalview/renderer/OverviewResColourFinder.java
JAL-3718 Added digestonly key to getdown.txt to copy file to alt or release when building, and to be included in the getdown digest. This key is completely ignored by the getdown-launcher. Looks in j8/j11digestonly.

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    /getdown/lib/getdown-launcher-local.jar
    • binary
    /j11digestonly/htsjdk-2.12.0.jar
  1. … 5 more files in changeset.
JAL-2656 Java 8 compatible test for gzipped, refactored for unit test

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    /test/jalview/io/FileIOTester.java