jalview

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Commits this week: 17
Total Committers: 73
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Commits this week: 17

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Monday 20 Dec 2021
12:15 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3753 avoid appending unreplaced html content in help pages

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    /build.gradle
9:50 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3842 patch what’s new text

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    /help/help/html/whatsNew.html
8:04 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3842 release 2.11.1.5 release notes

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    /help/help/html/releases.html
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    /help/help/html/whatsNew.html
7:45 am

Jim Procter <j.procter@dundee.ac.uk>

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

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Wednesday 15 Dec 2021
1:23 pm

Ben Soares

JAL-3933 updated THIRDPARTYLIBS

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    /THIRDPARTYLIBS
1:23 pm

Ben Soares

JAL-3933 updated THIRDPARTYLIBS

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    /THIRDPARTYLIBS
1:16 pm

Ben Soares

JAL-3933 updated THIRDPARTYLIBS

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    /THIRDPARTYLIBS
1:16 pm

Ben Soares

JAL-3933 updated THIRDPARTYLIBS

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    /THIRDPARTYLIBS
10:38 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3933 remove obsolete Castor logging configuration

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    /src/jalview/bin/Cache.java
10:38 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3933 remove obsolete Castor logging configuration

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    /src/jalview/bin/Cache.java
10:36 am

Jim Procter <j.procter@dundee.ac.uk>

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

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    /src/jalview/bin/Cache.java
10:36 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3933 configure root logger console appender to stderr

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    /src/jalview/bin/Cache.java
Tuesday 14 Dec 2021
11:23 pm

Ben Soares

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-14.31.53.jar
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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/log4j-to-slf4j-2.0-rc2.jar
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    /j11lib/slf4j-api-1.7.26.jar
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    /j11lib/slf4j-api-1.7.32.jar
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    /j11lib/slf4j-log4j12-1.7.26.jar
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    /j11lib/slf4j-log4j12-1.7.32.jar
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    /j8lib/Jmol-14.31.53.jar
    • binary
    /j8lib/Jmol-NO_LOG4J-14.31.53.jar
  16. … 13 more files in changeset.
8:31 pm

Ben Soares

JAL-3933 updated slf4j to 1.7.32

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    /j11lib/slf4j-api-1.7.26.jar
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    /j11lib/slf4j-api-1.7.32.jar
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    /j11lib/slf4j-log4j12-1.7.26.jar
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    /j11lib/slf4j-log4j12-1.7.32.jar
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    /j8lib/slf4j-api-1.7.26.jar
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    /j8lib/slf4j-api-1.7.32.jar
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    /j8lib/slf4j-log4j12-1.7.26.jar
    • binary
    /j8lib/slf4j-log4j12-1.7.32.jar
8:00 pm

Ben Soares

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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    /j11lib/log4j-to-slf4j-2.0-rc2.jar
    • binary
    /j8lib/jabaws-min-client-2.2.0.jar
    • binary
    /j8lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j8lib/log4j-1.2-api-2.16.0.jar
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    /j8lib/log4j-api-2.16.0.jar
    • binary
    /j8lib/log4j-core-2.16.0.jar
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    /j8lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j8lib/log4j-to-slf4j-2.0-rc2.jar
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    /j8lib/slf4j-api-1.7.26.jar
  16. … 4 more files in changeset.
Monday 13 Dec 2021
6:19 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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6:17 pm

Jim Procter <j.procter@dundee.ac.uk>

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
5:49 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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5:49 pm

Jim Procter <j.procter@dundee.ac.uk>

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
4:54 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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    /build.gradle
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    /gradle.properties
4:54 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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    /build.gradle
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    /gradle.properties
4:26 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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2:15 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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    /src/jalview/structure/StructureSelectionManager.java
Wednesday 08 Dec 2021
6:58 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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6:53 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551 pymol docs - work in progress

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    /help/help/help.jhm
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    /help/help/helpTOC.xml
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    /help/help/html/features/chimera.html
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    /help/help/html/features/pymol.html
6:52 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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    /src/jalview/structure/StructureSelectionManager.java
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    /src/mc_view/PDBChain.java
3:59 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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    /resources/lang/Messages.properties
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/PymolViewer.java
3:48 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551 JAL-3931 view pymol commands/responses in Log.trace

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    /src/jalview/ext/pymol/PymolManager.java
3:45 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3931 remove % and - from ids so Pymol doesn’t strip them out and truncate the structure identifier that Jalview uses to refer to each file

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    /src/jalview/gui/PymolBindingModel.java
3:44 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 URLencode pdbid to remove problematic characters - propagate urlEncoded ID to the features transferred from the structure file

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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/ws/dbsources/EBIAlfaFold.java
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    /src/mc_view/PDBChain.java