jalview

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JAL-3680 merged description of individual cursor key actions

JAL-3732 - sequences can be moved up/down in cursor mode via alt-up/down arrow JAL-3733 TODO - provide an undo for sequence/group up/down moves

JAL-3732 - sequences can be moved up/down in cursor mode via alt-up/down arrow JAL-3733 TODO - provide an undo for sequence/group up/down moves

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

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    /resources/images/JalviewConsole.png
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    /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