jalview

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Merge branch 'develop' into task/JAL-3911_getdown_improvements

JAL-3594 correct Jalview Develop logo SVG added in [not actually used in application]

JAL-3926 disable autosearch by default

JAL-3911 updated JARs for getdown

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    /getdown/lib/getdown-launcher-local.jar
JAL-3911 HiDPISetting update. jalview.bin.* update. Attempt to detect SHIFT key -- Order of app config and window appearance wrong. must create a window to click instead.

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

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

    • -0
    • +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-3746 Updated help docs for 3D-Beacons. Added and altered images and text.

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    /help/help/html/features/3dbeacons_button.png
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    /help/help/html/features/3dbeacons_structurechooser.png
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    /help/help/html/features/3dstructuredata_popupmenu.png
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    /help/help/html/features/schooser_main.png
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    /help/help/html/features/schooser_viewbutton.png
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    /help/help/html/features/selectfetchdb.gif
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    /help/help/html/features/seqfetch.html
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    /help/help/html/features/seqfetcher.gif
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    /help/help/html/features/structurechooser.html
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    /help/help/html/features/viewingpdbs.html
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' of https://source.jalview.org/git/jalview into develop

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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    /test/jalview/gui/StructureChooserTest.java
JAL-3907 changed two commented out lines to reflect location of future upgraded JRE zipfiles.

JAL-3907 added creation of symbolic links to workaround an install4j9 problem with parsing packed jre filenames with hyphens.

JAL-3907 adjusted download_jdks.sh and download_jres.sh scripts to use adoptium and added Java 17 download. Added JAVA_VERSION=17 as a gradle build property option.

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

    • -4
    • +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-3616 show name of structure viewer in ‘new view’ button

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    • +5
    /src/jalview/jbgui/GStructureChooser.java
JAL-3616 explicit configure external viewer config

Merge branch 'develop' into releases/Release_2_11_2_Branch