jalview

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JAL-3692 unit test updated for ?gzip download endpoint URL

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    /test/jalview/ws/ebi/EBIFetchClientTest.java
JAL-3692 parse multiline feature qualifiers and escaped quotes

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    /src/jalview/io/EmblFlatFile.java
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    /src/jalview/ws/ebi/EBIFetchClient.java
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    /test/jalview/io/EmblFlatFileTest.java
JAL-3692 set CDS /product as EMBLCDSPROTEIN description

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    /test/jalview/io/EmblFlatFileTest.java
JAL-3692 refactor/complete parsing, more unit test coverage

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    /src/jalview/io/EmblFlatFile.java
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    /src/jalview/ws/dbsources/EmblCdsSource.java
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    /src/jalview/ws/dbsources/EmblSource.java
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    /src/jalview/ws/dbsources/EmblXmlSource.java
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    /test/jalview/io/EmblFlatFileTest.java
JAL-3692 parse DE for description, and other refactoring...

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    /src/jalview/io/EmblFlatFile.java
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    /test/jalview/io/EmblFlatFileTest.java
JAL-3692 URL tests updated

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    /test/jalview/ws/ebi/EBIFetchClientTest.java
JAL-3692 unit test (J03321), fixes, dbrefs; todo: protein mappings

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    /src/jalview/io/EmblFlatFile.java
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    /test/jalview/io/EmblFlatFileTest.java
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    /test/jalview/io/J03321.embl.txt
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)

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    /resources/lang/Messages_es.properties
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    /src/jalview/io/EmblFlatFile.java
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    /src/jalview/util/MappingUtils.java
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    /src/jalview/ws/dbsources/EmblCdsSource.java
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    /src/jalview/ws/dbsources/EmblFlatfileSource.java
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    /src/jalview/ws/dbsources/EmblSource.java
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    /src/jalview/ws/dbsources/EmblXmlSource.java
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    /src/jalview/ws/ebi/EBIFetchClient.java
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    /test/jalview/util/MappingUtilsTest.java
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    /test/jalview/ws/dbsources/EmblXmlSourceTest.java
JAL-1424 streamlined message checker, corrected applet lookup keys

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AppletJmol.java
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    /utils/MessageBundleChecker.java
JAL-1424 slight tidying of reporting

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    /utils/MessageBundleChecker.java
JAL-3311 JAL-3141 JAL-3144 tidying obsolete message bundle entries

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/fts/core/FTSRestClient.java
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    /src/jalview/gui/VamsasApplication.java
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    /src/jalview/io/VamsasAppDatastore.java
JAL-3518 Spanish text for 'write features'

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    /resources/lang/Messages_es.properties
JAL-3570 JAL-3187 spanish translations for tabbed feature settings

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    /resources/lang/Messages_es.properties
JAL-3570 updated external help links

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    /help/help/html/webServices/AACon.html
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    /help/help/html/webServices/msaclient.html
Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

JAL-3675 2.11.1.1 release notes

JAL-3493 clear search highlights when escape/deselect all

JAL-3493 failing test - creates a highlight and column selection and then called the deselect all alignfjame action and checks if highlight and selection are still present. Conflicts: test/jalview/gui/SeqCanvasTest.java

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    /test/jalview/gui/SeqCanvasTest.java
JAL-3674 more finessed asynchronous structure commands

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

JAL-3518 corrected pulled up focusView() command

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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3518 corrected action on pulled up closeViewer()

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    /src/jalview/gui/StructureViewerBase.java
JAL-3551 PyMOL command constants tidied

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    /src/jalview/ext/pymol/PymolCommands.java
JAL-3551 fit to window (zoom) command for PyMOL

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    /src/jalview/ext/pymol/PymolCommands.java
JAL-3673 make sure font metrics are updated if dealing with reference sequence font !

JAL-3518 fix highlighting in Jalview for selections in ChimeraX - needed to thread off the subsequent POST back to ChimeraX so ChimeraX can first hangup its GET to Jalview’s Rest API

JAL-3672 debug=false means no debug output

JAL-3672 more efficient when debug not enabled

JAL-3671 hardwire log4j.root logger to INFO to supress jetty and httpclient log output

JAL-3518 tidy up asynchronous structure command execution