jalview

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JAL-3753 avoid appending unreplaced html content in help pages

JAL-3842 patch what’s new text

JAL-3842 release 2.11.1.5 release notes

Merge branch 'critical/JAL-3933_log4shell_mitigation' into releases/Release_2_11_1_Branch

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 remove obsolete Castor logging configuration

JAL-3933 configure root logger console appender to stderr

JAL-3933 updated slf4j to 1.7.32

    • binary
    /j11lib/slf4j-api-1.7.32.jar
    • binary
    /j11lib/slf4j-log4j12-1.7.32.jar
    • binary
    /j8lib/slf4j-api-1.7.32.jar
    • binary
    /j8lib/slf4j-log4j12-1.7.32.jar
JAL-3933 Updated log4j jars with log4j-2.16.0 and compatibility API log4j-1.2-api-2.16.0. Stripped log4j classes from jabaws-min-client jar. Updated sl4j jars in j8lib

    • binary
    /j11lib/jabaws-min-client-2.2.0.jar
    • binary
    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j11lib/log4j-1.2-api-2.16.0.jar
    • binary
    /j11lib/log4j-api-2.16.0.jar
    • binary
    /j11lib/log4j-core-2.16.0.jar
    • binary
    /j11lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j8lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j8lib/log4j-1.2-api-2.16.0.jar
    • binary
    /j8lib/log4j-api-2.16.0.jar
    • binary
    /j8lib/log4j-core-2.16.0.jar
    • binary
    /j8lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j8lib/slf4j-api-1.7.26.jar
  1. … 4 more files in changeset.
JAL-3842 fix automatic what's new link for custom version builds

JAL-3842 JAL-3746 (need to cherry pick to develop) - automatically generate link to latest release notes in what's new

JAL-3842 2.11.1.5 what’s new, release notes, and version bump

Merge branch 'patch/JAL-3840_2_11_1_4' into releases/Release_2_11_1_Branch

JAL-3840 don’t update the modal residue count for gaps

    • -1
    • +6
    /src/jalview/datamodel/ResidueCount.java
fixes JAL-3840

    • -9
    • +1
    /src/jalview/datamodel/ResidueCount.java
JAL-3840 failing test - show that addGaps overflows

    • -1
    • +1
    /src/jalview/datamodel/ResidueCount.java
JAL-3248 Archived old README. Added new README to point user to doc/building.md

    • -0
    • +47
    /doc/old_ant_build_README
JAL-3743 Fixed NullPointerExceptions happening with linkCheck task when gradle >= 6.6

JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values

JAL-3816 release date updated to 9th March

JAL-3816 release date set for 8th March and updated what's new

JAL-3816 new known defects JAL-3705 and JAL-3806

Revert "Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch"

This reverts commit cb628aab46f9027e71b71203b322f96710e09990, reversing

changes made to a40669b2eeb34a6c760b63c172a31a194b456f24.

    • -111
    • +20
    /test/jalview/util/MappingUtilsTest.java
Revert "JAL-3816 release notes for JAL-3806"

This reverts commit ead40d75a04715c80c61e34e277bb995cb2bef90.

JAL-3816 release notes for JAL-3806

Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch

JAL-3816 JAL-3814 JAL-3813 JAL-3812 JAL-3811 JAL-3818 release notes and date for 2.11.1.4 release

Merge branch 'bug/JAL-3818_jmolDeadlock' into releases/Release_2_11_1_Branch

Merge branch 'releases/Release_2_11_1_4_debianpatches' into releases/Release_2_11_1_Branch