jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3989 slight refactor of build.gradle, add more metadata to JSON file. Added some commented out path changes to gradle.properties for future gathering of built files into more sensible places

JAL-3989 fix a build date once in build.gradle, not each time getDate() is called.

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3983 release note for JAL-3985

Merge branch 'bug/JAL-3085_avoid_414_error_for_PDBFTS' into develop

Merge branch 'task/JAL-3553_improved_install4j_output_txt' into merge/JAL-3978+JAL-3553+develop

Merge branch 'develop' into improvement/JAL-3978_add_gradle_task_to_make_getdown_archive_dir

JAL-3085 update tests and mock responses, new P0dtd1 testcase

JAL-3985 formatting

JAL-3985 split PDB id queries into multiple queries so server doesn’t 414

Merge branch 'feature/JAL-3982_mouseover_highlighting_viaJAL-3860' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

JAL-3847 Add some dependencies that gradle 7 mildly complains about

Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop

JAL-3976 fix mock PDBFTS query & responses

JAL-3983 known issue note for JAL-3984

JAL-3851 comment out some debugging

JAL-3983 release notes for JAL-3975 and known issue note for JAL-3984

Merge branch 'bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog' into develop

JAL-360 JAL-3975 update parent for text colour dialog - doesn't seem to help but we live in hope..

    • -7
    • +7
    /src/jalview/gui/TextColourChooser.java
JAL-3983 update release notes for JAL-3973

JAL-3973 exclude the original RELEASE file so gradle doesn't complain of duplicate entries in the tarball

Merge branch 'bug/JAL-3973_source_tarball_not_building' into develop

JAL-3983 release 2.11.2.1 date and release notes

JAL-3982 todo notes

JAL-3860 prototype for highlight species/assembly/chromosome/position

    • -0
    • +126
    /src/jalview/rest/HighlightGenomicRangeEndpoint.java
JAL-3982 JAL-3860 encapsulate genomic coordinates mapping/liftover logic

JAL-3860 JAL-3892 extract genomic assembly mapping logic to static store

    • -0
    • +158
    /src/jalview/datamodel/GenomicAssemblies.java
    • -148
    • +2
    /src/jalview/io/vcf/VCFLoader.java
JAL-3851 Some streamlining of caching/removing from cache. 'Highlighting' in InputAlignment endpoint windows

    • -0
    • +12
    /src/jalview/gui/CutAndPasteTransfer.java
    • -3
    • +8
    /src/jalview/rest/AbstractEndpoint.java
    • -0
    • +36
    /src/jalview/rest/AbstractEndpointAsync.java
    • -1
    • +1
    /src/jalview/rest/FetchSequencesEndpoint.java
    • -1
    • +1
    /src/jalview/rest/InputAlignmentEndpoint.java
JAL-3851 Add a redirect back to itself for working endpoints

    • -0
    • +24
    /src/jalview/rest/AbstractEndpoint.java
    • -2
    • +34
    /src/jalview/rest/AbstractEndpointAsync.java
    • -0
    • +3
    /src/jalview/rest/FetchSequencesEndpoint.java
JAL-3878 Patch preferences window to use new discoverer.

    • -34
    • +37
    /src/jalview/gui/SlivkaPreferences.java