jalview

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JAL-3821 ported to refactored FlatFile parser

JAL-3821 failing test

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    /test/jalview/io/EmblFlatFileTest.java
JAL-3692 JAL-3861 remove extra call to .parse() so we don’t process the file again

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'patch/JAL-3874_newJmolAndGradleDedup' into develop

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3851 api_specification.md in progress

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    /doc/api_specification.md
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-3878 Implement AlignmentOperation WIP

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    /src/jalview/ws2/operations/AlignmentOperation.java
JAL-3878 Create interface for web service operations

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    /src/jalview/ws2/operations/Operation.java
JAL-3878 Implement slivka web service and discoverer.

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    /src/jalview/ws2/slivka/SlivkaWS.java
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    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Add web service executor class and instantiate for each alignment viewport.

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    /src/jalview/ws2/WebServiceExecutor.java
JAL-3878 Create base interfaces for new web services.

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    /src/jalview/ws2/JalviewWebServiceI.java
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    /src/jalview/ws2/MenuEntryProviderI.java
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    /src/jalview/ws2/MsaMenuEntryProvider.java
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    /src/jalview/ws2/ResultSupplier.java
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    /src/jalview/ws2/WSJob.java
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    /src/jalview/ws2/WSJobStatus.java
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    /src/jalview/ws2/WebServiceDiscoverer.java
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    /src/jalview/ws2/WebServiceI.java
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    /src/jalview/ws2/WebServiceInfoUpdater.java
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    /src/jalview/ws2/WebServiceThreadListenerI.java
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    /src/jalview/ws2/WebServiceWorkerI.java
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    /src/jalview/ws2/utils/WSJobList.java
JAL-3878 Remove throws declaration from param store construction.

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    /src/jalview/ws/slivkaws/SlivkaParamSet.java
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