jalview

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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
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
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
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

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    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/file_associations_template-install4j8.xml
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

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    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/file_associations_template-install4j8.xml
Merge branch 'develop' into task/JAL-3911_getdown_improvements

JAL-3904 use new AlignPanel API method

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    /src/jalview/gui/ViewSelectionMenu.java
JAL-3904 simple method to make an alignPanel the currently viewed one in the alignframe

JAL-3878 Use annotations from the representative sequence in the new alignment.

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    /src/jalview/ws2/gui/JPredMenuBuilder.java
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    /src/jalview/ws2/operations/JPredWorker.java
JAL-3594 correct Jalview Develop logo SVG added in [not actually used in application]

JAL-3927 Make url checks asynchronous in preferences dialog

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    /src/jalview/gui/SlivkaPreferences.java
JAL-3878 Add jpred operation and worker to the services.

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    /src/jalview/ws2/gui/JPredMenuBuilder.java
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    /src/jalview/ws2/operations/JPredOperation.java
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    /src/jalview/ws2/operations/JPredWorker.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3553 added filesize to json

JAL-3878 Make openEditsParamsDialog an interface static method.

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    /src/jalview/ws2/gui/AnnotationMenuBuilder.java
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    /src/jalview/ws2/gui/MenuEntryProviderI.java
JAL-3066 Fix ambiguous assertEquals casting values to double.

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    /test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
JAL-3878 Add annotation operation and worker to the services.

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    /src/jalview/ws2/gui/AnnotationMenuBuilder.java
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    /src/jalview/ws2/gui/ProgressBarUpdater.java
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    /src/jalview/ws2/operations/AnnotationWorker.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java