jalview

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Merge branch 'releases/Release_2_11_1_Branch'

JAL-3842 remove replacement tokens in html text - not properly resolved in this release branch

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 updated THIRDPARTYLIBS

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 remove obsolete Castor logging configuration

JAL-3933 remove obsolete Castor logging configuration

JAL-3933 configure root logger console appender to stderr (2.11.2 version)

JAL-3933 configure root logger console appender to stderr

JAL-3933 updated log4j and slf4j jars with log4j1.2 compatibility API jar. Removed log4j from jabaws-min-client and Jmol jars

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    /j11lib/Jmol-NO_LOG4J-14.31.53.jar
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    /j11lib/jabaws-min-client-2.2.0.jar
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    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
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    /j11lib/log4j-1.2-api-2.16.0.jar
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    /j11lib/log4j-api-2.16.0.jar
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    /j11lib/log4j-core-2.16.0.jar
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    /j11lib/log4j-slf4j18-impl-2.16.0.jar
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    /j11lib/slf4j-api-1.7.32.jar
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    /j11lib/slf4j-log4j12-1.7.32.jar
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    /j8lib/Jmol-NO_LOG4J-14.31.53.jar
  1. … 13 more files in changeset.
JAL-3933 updated slf4j to 1.7.32

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    /j11lib/slf4j-api-1.7.32.jar
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    /j11lib/slf4j-log4j12-1.7.32.jar
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    /j8lib/slf4j-api-1.7.32.jar
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    /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

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    /j11lib/jabaws-min-client-2.2.0.jar
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    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
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    /j11lib/log4j-1.2-api-2.16.0.jar
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    /j11lib/log4j-api-2.16.0.jar
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    /j11lib/log4j-core-2.16.0.jar
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    /j11lib/log4j-slf4j18-impl-2.16.0.jar
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    /j8lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
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    /j8lib/log4j-1.2-api-2.16.0.jar
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    /j8lib/log4j-api-2.16.0.jar
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    /j8lib/log4j-core-2.16.0.jar
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    /j8lib/log4j-slf4j18-impl-2.16.0.jar
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    /j8lib/slf4j-api-1.7.26.jar
  1. … 4 more files in changeset.
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3829 isCanonical should by default be false - ensure JalviewJS offers 3d-beacons search for example project

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    /src/jalview/datamodel/DBRefEntry.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve been given it

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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/ws/dbsources/EBIAlfaFold.java
JAL-3746 update Jalview 2.12 branch from build.gradle for 2.11.2

JAL-3746 update Jalview 2.12 branch from build.gradle for 2.11.2

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3929 preserve lowercase pdbid in group name for transferred features

Merge branch 'to_merge/r2_11_2/JAL-3904_improved_alignpanelAPI_autoshowview' into develop

JAL-3551 pymol docs - work in progress

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    /help/help/html/features/pymol.html
JAL-3929 don’t use the url encoded pdbId in feature group when transferring features from associated structure to a sequence

JAL-3616 update messages/tooltips/menu items to use getViewerName() for chimera/x/pymol

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    /src/jalview/gui/ChimeraViewFrame.java
JAL-3551 JAL-3931 view pymol commands/responses in Log.trace

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    /src/jalview/ext/pymol/PymolManager.java