jalview

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JAL-3675 update release date and release notes for JAL-3280

Merge branch 'improvement/JAL-3280_Migrate_the_VersionChecker_service_to_build_properties' into releases/Release_2_11_1_Branch

JAL-3675 whats new, logging and release notes tidying for 2.11.1.1.

JAL-3676 rework logging docs.

Merge branch 'bug/JAL-3718_Getdown_does_not_autoupdate_correctly' into releases/Release_2_11_1_Branch

JAL-3676 remove mention of Castor

JAL-3675 tweak release notes for JAL-3667, JAL-3702

JAL-3675 update sequence fetcher service documentation for JAL-3692 (ENA Flatfile) and refreshed links for other endpoints.

    • -9
    • +25
    /help/help/html/features/seqfetch.html
JAL-3280 Test for remote release build_properties file version check

    • -0
    • +2
    /test/jalview/bin/testProps.jvprops
JAL-3280 fixes after CR-JAL-241. Now only checking release build_properties.

JAL-3280 Pass appbase and appdir from getdown to jalvew. Check appbase (defaults to release appbase) for build_properties VERSION insteadl of jnlp file.

JAL-3680 merged description of individual cursor key actions

JAL-3732 - sequences can be moved up/down in cursor mode via alt-up/down arrow JAL-3733 TODO - provide an undo for sequence/group up/down moves

JAL-3676 adding Axis and Castor loggging properties to the help text

JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs

Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch

    • -26
    • +0
    /src/jalview/gui/AlignViewport.java
report JAL-3127 as known defect (fix targeted for 2.11.2)

JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam

    • -13
    • +44
    /test/jalview/io/FileIOTester.java
JAL-3718 Added digestonly key to getdown.txt to copy file to alt or release when building, and to be included in the getdown digest. This key is completely ignored by the getdown-launcher. Looks in j8/j11digestonly.

    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /j11digestonly/htsjdk-2.12.0.jar
  1. … 5 more files in changeset.
JAL-3692 parse multiline CDS location correctly

    • -1
    • +9
    /test/jalview/io/EmblFlatFileTest.java
JAL-3676 Start of documentation in help pages logging.html

    • -0
    • +66
    /help/help/html/logging.html
JAL-3675 release notes for JAL-3691

Merge branch 'patch/JAL-3691_No_score_models_available' into releases/Release_2_11_1_Branch

JAL-3675 JAL-3561 documented in release notes

JAL-3675 report JAL-3702 as known defect

Merge branch 'patch/JAL-3561_JAL-3660_fileformatexport_CLI' into releases/Release_2_11_1_Branch

JAL-3712 fix typos for rebuilding/updating getdown jars and added mention of mvn_cmd in the getdown building help.

JAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documentation for 2.11.1.1

    • -9
    • +11
    /help/help/html/features/search.html
    • binary
    /help/help/html/features/search.png
Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_1_Branch

    • -0
    • +2
    /resources/lang/Messages_es.properties
    • -2
    • +1
    /src/jalview/gui/AnnotationColumnChooser.java
JAL-3675 JAL-3597 release notes