jalview

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JAL-3613 remove debug code committed in error

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    /src/jalview/util/BrowserLauncher.java
JAL-3613 check sequence overlap when matching search results

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    /src/jalview/datamodel/SearchResults.java
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    /src/jalview/util/BrowserLauncher.java
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3407 add GPL license to Jalview source files

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    /src/jalview/analysis/GeneticCodeI.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/bin/JalviewTaskbar.java
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    /src/jalview/bin/MemorySetting.java
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    /src/jalview/datamodel/GeneLociI.java
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    /src/jalview/datamodel/GeneLocus.java
  1. … 29 more files in changeset.
JAL-3407 release notes - JAL-247 - for auto-set-ID, and revise wording for transferring virtual features in chimera

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3407 fix JAL-3574 - remove from known issues for 2.11.1.0

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3574 JAL-3407 release notes

Merge branch 'bug/JAL-3574filterByPOS' into documentation/JAL-3407_2.11.1_release

Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3407 add and document ComputePeptideVariants.groovy

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    /examples/groovy/ComputePeptideVariants.groovy
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    /help/help/html/features/importvcf.html
JAL-3577 changed default RELEASE dir in build.gradle to use absolute path to help buildship when importing project for first time

Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

JAL-3567 JAL-3407 document sequence features report and the additional info provided for virtual features. Also bumped release date to 22st April

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    /help/help/html/features/seqfeaturereport.html
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    /help/help/html/features/seqfeaturesrep.png
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    /help/help/html/features/splitView.html
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    /help/help/html/menus/popupMenu.html
JAL-3577 Added newer install dirs to the deletion list in the uninstaller and tidied the list

Merge branch 'bug/JAL-3567virtualFeatureCoordinates' into develop

JAL-367 code tidy

JAL-3567 translated rather than imputed peptide

JAL-3567 unit tests for linked feature tooltips

JAL-3567 adjust layout of linked feature report, unit test

JAL-3567 added 'imputed by Jalview' to protein consequence in report

JAL-3567 report mapped location for virtual features in tooltip etc

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/io/FeaturesFile.java
JAL-3407 JAL-3529 release notes

Merge branch 'bug/JAL-3529_uniprotidsinstockholm' into develop

JAL-3529 revert ordering of DBRef addition so it reflects situation after Pfam import </picky>

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    /test/jalview/io/StockholmFileTest.java
JAL-3597 improved Memory test suite by detecting base memory usage rather than assuming it is constant for each release.

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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3407 release date set to 16th April, known issue report for JAL-3574

Merge branch 'testing/JAL-3577_jalviewversion_autoset_fixed' into develop

JAL-3574 test coverage corners

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    /test/jalview/util/matcher/MatcherTest.java