jalview

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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
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
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-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo

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    /j11lib/Jmol-14.31.53-dedup.jar
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    /j11lib/Jmol-14.31.53.jar
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    /j8lib/Jmol-14.31.53-dedup.jar
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    /j8lib/Jmol-14.31.53.jar
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-3874 attempt to add source jars to eclipse through buildship

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    /j11sources/Jmol-14.31.53-sources.jar
JAL-3829 belt and braces check to make sure there is a pdbe response available to join records from

JAL-3779 Added to documentation

JAL-3871 replaced Jmol with zip -F version fo Jmol and added excludeDuplicates flags to build.gradle

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    /j11lib/Jmol-14.31.53-dedup.jar
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    /j11lib/Jmol-14.31.53.jar
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    /j8lib/Jmol-14.31.53-dedup.jar
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    /j8lib/Jmol-14.31.53.jar