jalview

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Integration of Freemarker API to the Jalview help system to aid self-documentation where possible using predefined templates and boiler-plates codes from Jalview codebase

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    /help/freemarker_templates/alignmentMenu.ftl
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    /src/jalview/datamodel/DBRefSource.java
Merge branch 'bug/JAL-1558' into develop

Merge branch 'bug/JAL-1558' into Release_2_8_2_Branch_i18n

Merge branch 'bug/JAL-1558' into Release_2_8_2_Branch

patch fixes JAL-1558

patch fixes JAL-1558

Integration of Freemarker API to the Jalview help system to aid self-documentation where possible using predefined templates and boiler-plates codes from Jalview codebase

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    /help/html/menus/alignmentMenu.html
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    /src/jalview/help/freemarker/AllignmentMenuTemplateData.java
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    /src/jalview/io/AppletFormatAdapter.java
Merge branch 'Release_2_8_2_Branch' into features/JAL-1264_showHideAnnotations

Conflicts:

resources/lang/Messages.properties

src/jalview/datamodel/Alignment.java

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/gui/FeatureSettings.java
Merge branch 'bugs/JAL-1151' into develop

Merge branch 'bugs/JAL-1151' into Release_2_8_2_Branch_i18n

Merge branch 'bugs/JAL-1151' into Release_2_8_2_Branch

JAL-1557 partial implementation - need to think about how to do SHIFT+double click type range selections

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    /src/jalview/gui/AnnotationLabels.java
patch for JAL-1151 - select whole sequence when double clicking on associated annotation's id

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    /src/jalview/gui/AnnotationLabels.java
JAL-1421 remove Vector and pass a list

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    /src/jalview/gui/AnnotationLabels.java
JAL-1151 source tidy

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/AlignmentI.java
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    /src/jalview/datamodel/SequenceGroup.java
JAL-1554 handle left-then-right click on sequence id

Merge branch 'Release_2_8_2_Branch' into Release_2_8_2_Branch_i18n

Merge branch 'JAL-429_phylip-file-support' into develop

Merge branch 'JAL-429_phylip-file-support' into Release_2_8_2_Branch

Merge branch 'patch/JAL-848' into JAL-429_phylip-file-support

Merge branch 'patch/JAL-848' into Release_2_8_2_Branch

JAL-848 reinstate netbeans files from Phylip patch branch

Merge branch 'JAL-429_phylip-file-support' into Release_2_8_2_Branch

Merge branch 'Release_2_8_2_Branch' into JAL-429_phylip-file-support

Conflicts:

src/jalview/io/AppletFormatAdapter.java

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    /src/jalview/io/AppletFormatAdapter.java
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    /src/jalview/io/JalviewFileChooser.java
Merge branch 'patch/JAL-1286_JAL-1265' into Release_2_8_2_Branch_i18n

Merge branch 'patch/JAL-1286_JAL-1265' into develop

Merge branch 'patch/JAL-1286_JAL-1265' into Release_2_8_2_Branch

JAL-1500 JAL-1265 patch to parse PDB database refs in PFAM stockholm

JAL-1286 missing file for testcase where file ends in gz but isn't a gz file

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    /test/jalview/io/test_gz_fasta_notgz.gz