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jim procter <j.procter@dundee.ac.uk> in jalview

JAL-3926 disable autosearch by default

JAL-3923 JAL-3878 disable clover for CI builds

JAL-3922 convert selection events in Jmol to highlights in Jalview - still need to ignore selection events performed as part of Jalview manipulating Jmol.

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    • +81
    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    • +10
    /src/jalview/gui/AppJmolBinding.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3855 verify pdb suffix is preserved when locally loaded file is saved in project and imported

JAL-3855 JAL-1731 reuse the StructureViewer.fetchPdbFile(PDBEntry) method in JmolBinding - avoid code duplication for retrieval and import of 3d data

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    • +7
    /src/jalview/gui/AppJmolBinding.java
JAL-3855 try harder to ignore DNA/RNA only structures when deciding whether to download from SIFTS

JAL-3921 wait around until session file has been written

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    • +17
    /src/jalview/gui/StructureViewerBase.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3829 remove duplicate IDs in 3DBeacons generated PDBFTS query and update mocks

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3829 format and tidy up unused code

JAL-3919 use model format field to ensure we get the file extension correct when creating temp files for structure viewers

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    • +1
    /resources/fts/tdbeacons_data_columns.txt
JAL-3875 fully reset filter combo-box when fetch 3d-beacons button is pressed, and ensure first 3d-beacons option selected when structures are discovered even when cached structures are present.

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    • +16
    /src/jalview/gui/StructureChooser.java
JAL-3915 JAL-3746 documentation for removed rnaview options

JAL-3916 TODO for improved selection of covering structures

JAL-3916 TODO for improved selection of covering structures

JAL-3915 remove RNAview opts from preferences. Still present in config file ready for when we have a new RNA structure processing service

Merge branch 'develop' into releases/Release_2_11_2_Branch

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3875 test case and patch to verify the query 3d beacons button is shown for proteins with uniprot ids but no canonical accessions

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    • +14
    /src/jalview/gui/StructureChooser.java
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    • +23
    /test/jalview/gui/StructureChooserTest.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'bug/r2_11_2/JAL-3904_structureviewermenu' into develop

JAL-3905 Fix: wait for response when sending mouseovers. Combined remove old label and add new label and also added warning in javadoc about out-of-order execution

JAL-3904 override buildActionMenu to add in additional menu actions after rebuild

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    • +15
    /src/jalview/gui/ChimeraViewFrame.java
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    • +7
    /src/jalview/gui/StructureViewerBase.java
JAL-3904 failing test

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    • +5
    /src/jalview/gui/StructureViewerBase.java
JAL-2909 JAL-3894 hack in support to import regions of an unindexed SAM file.

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    • +10
    /src/jalview/datamodel/CigarParser.java
Merge branch 'develop' into features/JAL-2909_bamImport_2_11_2

Merge branch 'develop' into releases/Release_2_11_2_Branch