Clone Tools
  • last updated a few seconds ago
Constraints: committers
Constraints: files
Constraints: dates
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

    • binary
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

    • -43
    • +7
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

    • -2
    • +17
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
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.

    • -3
    • +16
JAL-3746 Updated help docs for 3D-Beacons. Added and altered images and text.

    • binary
    • binary
    • binary
    • binary
    • binary
    • binary
    • -2
    • +5
    • binary
    • -5
    • +43
    • -7
    • +18
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

    • -1
    • +14
    • -2
    • +23
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
    • -1
    • +7
JAL-3904 failing test

    • -1
    • +5
JAL-3616 show name of structure viewer in ‘new view’ button

    • -1
    • +5
JAL-3616 explicit configure external viewer config

Merge branch 'develop' into releases/Release_2_11_2_Branch