jalview

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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
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    /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
JAL-1260 refactored multi-line qualifier separators

JAL-1260 refactored multi-line qualifier separators

JAL-3692 parse multiline CDS location correctly

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    /test/jalview/io/EmblFlatFileTest.java
JAL-1260 unit test for FileFormats updated for GenBank/ENA

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    /test/jalview/io/FileFormatsTest.java
JAL-1260 unit test for FileFormats updated for GenBank/ENA

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    /test/jalview/io/FileFormatsTest.java
JAL-1260 file formats and IdentifyFile updates for GenBank and ENA

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    /test/jalview/io/EmblFlatFileTest.java
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    /test/jalview/io/IdentifyFileTest.java
JAL-1260 file formats and IdentifyFile updates for GenBank and ENA

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    /test/jalview/io/EmblFlatFileTest.java
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    /test/jalview/io/IdentifyFileTest.java
JAL-1260 refactored GenBank (and EMBL) flat file parser

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    /src/jalview/io/EmblFlatFile.java
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    /src/jalview/io/FlatFile.java
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    /src/jalview/io/GenBankFile.java
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    /test/jalview/io/EmblFlatFileTest.java
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    /test/jalview/io/GenBankFileTest.java
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    /test/jalview/io/J03321.gb
JAL-1260 refactored GenBank (and EMBL) flat file parser

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    /src/jalview/io/EmblFlatFile.java
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    /src/jalview/io/FlatFile.java
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    /src/jalview/io/GenBankFile.java
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    /test/jalview/io/EmblFlatFileTest.java
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    /test/jalview/io/GenBankFileTest.java
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    /test/jalview/io/J03321.gb
JAL-3676 Start of documentation in help pages logging.html

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    /help/help/html/logging.html
JAL-3675 release notes for JAL-3691

Merge branch 'patch/JAL-3691_No_score_models_available' into releases/Release_2_11_1_Branch

JAL-3675 JAL-3561 documented in release notes

JAL-3675 report JAL-3702 as known defect

Merge branch 'patch/JAL-3561_JAL-3660_fileformatexport_CLI' into releases/Release_2_11_1_Branch

JAL-3712 fix typos for rebuilding/updating getdown jars and added mention of mvn_cmd in the getdown building help.

JAL-3490 don't init the combo box's history cache for JS execution

JAL-3490 merged with 2.11.2 develop

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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/Finder.java
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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/datamodel/SearchResults.java
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    /src/jalview/gui/AlignViewport.java
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    /src/jalview/gui/AnnotationColumnChooser.java
  1. … 8 more files in changeset.
JAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documentation for 2.11.1.1

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    /help/help/html/features/search.html
    • binary
    /help/help/html/features/search.png
Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_1_Branch

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/AnnotationColumnChooser.java
Merge branch 'task/JAL-3597memoryLeakTest' into develop

JAL-3675 JAL-3597 release notes

Merge branch 'patch/JAL-3597_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch