jalview

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JAL-3679 Added externally specified plugins dir to J2sPlugin check

JAL-3679 Added externally specified plugins dir to J2sPlugin check

JAL-3679 Added externally specified plugins dir to J2sPlugin check

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

JAL-3576 IntervalStore updated to v1.2

    • binary
    /j11lib/intervalstore-v1.2.jar
    • binary
    /j8lib/intervalstore-v1.2.jar
    • -59
    • +68
    /test/jalview/io/vcf/VCFLoaderTest.java
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 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 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-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-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-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-3518 removed unneeded override in ChimeraCommands

    • -27
    • +0
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
JAL-3518 removed unneeded override in ChimeraCommands

    • -27
    • +0
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
JAL-3018 Ensembl reviewed REST version updated to 13.0

JAL-1191 use Cache.log for logging

    • -2
    • +2
    /src/jalview/ext/so/SequenceOntology.java
JAL-3730 retry ping before failing; sysout logging changed to Cache.log

    • -9
    • +10
    /src/jalview/ext/ensembl/EnsemblMap.java
    • -4
    • +4
    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-3676 adding Axis and Castor loggging properties to the help text

JAL-3725 restrict mapped virtual feature location to mapped region Conflicts: src/jalview/gui/PopupMenu.java