jalview

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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/Conservation.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/commands/EditCommand.java
  1. … 88 more files in changeset.
JAL-3746 release notes and what’s new for 2.11.2 - in progress

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    /help/help/html/features/preferences.html
Merge branch 'doc/JAL-3746_Release_2_11_2' into develop

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

JAL-3829 - callback finessing - leave DBRefFetcher to do progress updates itself

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    /src/jalview/gui/StructureChooser.java
JAL-3829 prefix PDBe filters with PDBe to make clear what they search

JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need to be fetched

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    /src/jalview/gui/StructureChooser.java
JAL-3521 'Debian-safe' version of minimal build.gradle and patch. Using existing doc/*.html and build_properties from source tarball.

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    /utils/debian/build_gradle.patch
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    /utils/debian/debian_build.gradle
JAL-3829 ignore the fake ID generated when a PDB format file without embedded ID is imported for an existing PDBEntry

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    /src/jalview/datamodel/PDBEntry.java
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    /test/jalview/datamodel/SequenceTest.java
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    /test/jalview/ext/jmol/JmolParserTest.java
JAL-3521 Created a patch file to transform build.gradle into debian_build.gradle

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    /utils/debian/build_gradle.patch
JAL-3829 updated response for P01308

JAL-3829 tests need to wait for dialog to be closed and background processes to finish before they can check functionality

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    /src/jalview/gui/StructureChooser.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 TDBeacons fetcher needs a sequence with at least one canonical uniprot accession

JAL-3829 throw the exception even if it has no message

JAL-3829 ensure nulls are not wildcards when retrieving annotation by calcId/label/description

JAL-3521 working minimal build.gradle for debian and 2.11.2. Flexmark plugin might be a problem

JAL-3521 not quite working minimal build.gradle for debian and 2.11.2

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    /utils/debian/debian_build.gradle
JAL-3829 do better at detecting structure type, prompt to retrieve Uniprot ids for proteins without canonical Ids and show provider in the Structure Chooser’s cache view

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    /resources/fts/tdbeacons_data_columns.txt
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    /src/jalview/gui/StructureChooser.java
JAL-3829 make sure structure data type reflects actual format identified

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    /src/jalview/ext/jmol/JmolParser.java
JAL-3829 store 3db metadata on PDBEntry so it can be shown in Cache/etc

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    /src/jalview/datamodel/PDBEntry.java
JAL-3829 allow PDBEntry with file and ID with mismatching case to override one without a file

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    /src/jalview/datamodel/PDBEntry.java
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    /test/jalview/datamodel/PDBEntryTest.java
Merge branch 'merge/develop_JAL-1260' into develop

JAL-1260 rudimentary parsing of LOCUS line to at least get accession id

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    /src/jalview/io/GenBankFile.java
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

JAL-3079 JAL-3055 remember to reset font transform after rendering logo

JAL-2226 transfer chain annotation when calcId, label and description are distinct - so annotations from multiple chains and structures are all shown.

JAL-2226 new method to search for annotation matching particular description as well as calcId and label

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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-3829 belt and braces check to make sure there is a pdbe response available to join records from

JAL-3779 Added to documentation