jalview

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JAL-1990 suggested revision to separate references to UI components from datamodel event broadast components

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AppletJmol.java
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    /src/jalview/appletgui/ExtJmol.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/StructureViewerBase.java
JAL-1993 close sequence fetcher when opening database chooser

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    /src/jalview/gui/SequenceFetcher.java
JAL-2124 JAL-1990 additional translations

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    /resources/lang/Messages_es.properties
JAL-2112 optimisation of EMBL CDS parsing

JAL-1993 hide sequence fetcher dialogue until database selection made

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    /src/jalview/gui/SequenceFetcher.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

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    /src/jalview/gui/StructureChooser.java
JAL-2002 disabled 'Best Uniport Coverage' filter. JAL-1990 i18n for status messages in the newly introduced progress indicator for Structure Chooser interface

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    /src/jalview/gui/StructureChooser.java
JAL-2025 unit tests added

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    /src/jalview/gui/StructureChooser.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-2101 unit test updated to match config file

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    /resources/fts/uniprot_data_columns.txt
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    /test/jalview/fts/core/FTSRestClientTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-2102 right justify 'Mass' in uniprot FTS, and 'Max Observed Residue' in PDB FTS, and correct 'Miscellaneous' spelling

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    /resources/fts/uniprot_data_columns.txt
JAL-2114 more helpful reporting of parse failures

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    /test/jalview/util/DnaUtilsTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-2047 trapped block that could likely cause ClassCastException

JAL-2047 resolved structure chooser's displayed column configuration updating, added horizontal scrollbar to structure chooser summary table and minor house keeping

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    /src/jalview/fts/api/FTSRestClientI.java
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    /src/jalview/fts/core/FTSRestClient.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
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    /test/jalview/fts/core/FTSRestClientTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-1479 updated SIFTS FTP download URL, added improvement to ensure that new SIFTS file are successfully downloaded before overwriting the outdated cached ones, and added fix for PDB RESNUM transfer via JMol parser

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    /src/jalview/ws/sifts/SiftsClient.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
Merge branch 'r291_docs' into develop

JAL-2089 docs for June 10th

JAL-1941 added test URL and notes about PyRNA restclient

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    /src/jalview/ext/paradise/Annotate3D.java
JAL-1941 Annotate3d tests should be in network group

JAL-2114 corrected Javadoc

JAL-1479 JAL- Fix to eradicate duplicate mapping output and further improvement for DBRef re-fetching and matching issue

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    /src/jalview/gui/AlignViewport.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2089 signed off bug release notes

JAL-1941 remove improper test tag from Annotate3D test helper

JAL-1919, JAL-1960 fix to disable refetching dbrefs when viewing structures

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    /src/jalview/gui/StructureChooser.java
JAL-1944 bugfix for wrong alignment numbering when exporting an alignment and export hidden sequences is enabled

JAL-2089 documenting for 8th june RC1

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

merge

JAL-2020 fix for Jmol choking jalview while loading a structure