jalview

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New jalview.log.JLogger logging framework. Remove jalview.javascript.log4j as no longer needed

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    /src/jalview/io/StockholmFile.java
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    /src/jalview/io/vamsas/DatastoreItem.java
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    /src/jalview/javascript/log4j/Layout.java
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    /src/jalview/javascript/log4j/Level.java
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    /src/jalview/javascript/log4j/core/Logger.java
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Merge branch 'bug/JAL-3523_cwd_not_preserved' into develop rebuilt getdown jars - did not bump version

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    /getdown/lib/getdown-launcher-local.jar
Put logging through Cache methods. Take 3

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    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/gui/PromptUserConfig.java
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    /src/jalview/gui/UserQuestionnaireCheck.java
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    /src/jalview/gui/VamsasApplication.java
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    /src/jalview/io/VamsasAppDatastore.java
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    /src/jalview/io/vamsas/DatastoreItem.java
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Put logging through Cache methods. Take 2

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    /src/jalview/gui/PromptUserConfig.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/UserQuestionnaireCheck.java
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    /src/jalview/gui/VamsasApplication.java
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    /src/jalview/gui/WsParamSetManager.java
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Put logging through Cache methods. Take 1

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/ext/ensembl/EnsemblLookup.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/ext/htsjdk/VCFReader.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/ext/so/SequenceOntology.java
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Allow logging with message and exception

streamline of Cache logging

streamlined Log4j usage

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    /src/jalview/javascript/log4j/Layout.java
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    /src/jalview/javascript/log4j/Logger.java
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    /src/jalview/javascript/log4j/core/Appender.java
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    /src/jalview/javascript/log4j/core/Logger.java
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    /src/jalview/javascript/log4j/core/net/Priority.java
JAL-3954 Prepare a skeleton for PHMMER web service.

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    /src/jalview/ws2/gui/PhmmerMenuBuilder.java
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    /src/jalview/ws2/hmmer/ParamSetFactory.java
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    /src/jalview/ws2/hmmer/PhmmerParamDatastore.java
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    /src/jalview/ws2/hmmer/PhmmerWSDiscoverer.java
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    /src/jalview/ws2/hmmer/PhmmerWebService.java
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    /src/jalview/ws2/operations/PhmmerOperation.java
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    /src/jalview/ws2/operations/PhmmerWorker.java
JAL-3954 Introduce hmmer rest client to jalview.

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    /src/jalview/hmmer/rest/FormURLEncodedBodyBuilder.java
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    /src/jalview/hmmer/rest/InputSequence.java
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    /src/jalview/hmmer/rest/PhmmerClient.java
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    /src/jalview/hmmer/rest/PhmmerRequest.java
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    /src/jalview/hmmer/rest/PhmmerRequestBuilder.java
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    /src/jalview/hmmer/rest/ResultType.java
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    /src/jalview/hmmer/rest/Status.java
slight streamline of log level name

Firm up last commit: correct application logger name back to original, fixes other addAppenders in Cache

correct application logger name back to original, fixes other addAppenders in Cache

Test to check for debug Log4j Test message

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    /test/jalview/util/Log4jTest.java
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    /test/jalview/util/log4jTestProps.jvprops
Correct output in SimpleLayout format for both stderr and Java console

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    /src/jalview/gui/JalviewAppender.java
Merge branch 'feature/JAL-1713_overviewInProject' into bug/JAL-3785autoOverviewTitle

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/project/Jalview2XML.java
JAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTitle' into 2_11_2_develop regenerated jaxb bindings for updated schemas on develop & feature branch Conflicts: src/jalview/gui/Preferences.java src/jalview/xml/binding/jalview/JalviewModel.java src/jalview/xml/binding/jalview/ObjectFactory.java src/jalview/xml/binding/jalview/package-info.java

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    /src/jalview/project/Jalview2XML.java
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    /src/jalview/xml/binding/embl/EntrySetType.java
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    /src/jalview/xml/binding/embl/EntryType.java
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    /src/jalview/xml/binding/embl/ROOT.java
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JAL-3186 remove ‘Variable Colour’ from the sequence feature settings popup menu

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    /src/jalview/gui/FeatureSettings.java
JAL-819 update branch 'feature/JAL-819undeleteAutoannotation' from 2.11.2 develop

Conflicts:

src/jalview/api/AlignViewportI.java

src/jalview/gui/AnnotationLabels.java

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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/jbgui/GAlignFrame.java
JAL-722 updated from 2.11.2 develop branch - needs further work before release

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/datamodel/Alignment.java

src/jalview/gui/AlignFrame.java

src/jalview/io/AlignFile.java

src/jalview/project/Jalview2XML.java

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    /resources/lang/Messages_es.properties
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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/datamodel/AlignmentI.java
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    /src/jalview/gui/AlignFrame.java
JAL-3949 An attempt at converting to Log4j 2 -- no output achieved!

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    /src/jalview/gui/JalviewAppender.java
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    /src/jalview/io/vamsas/DatastoreItem.java
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    /src/jalview/javascript/log4j/Layout.java
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    /src/jalview/util/Log4j.java
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    /src/jalview/util/MessageManager.java
JAL-3878 Fix typo in slivka host urls variable name.

Merge branch 'bug/JAL-3806_mappingCoversSequence_for2112' into develop Combines patches for JAL-3806 prior to redaction of shared CDS dataset sequences with patches for JAL-3673 Conflicts: src/jalview/datamodel/AlignedCodonFrame.java src/jalview/util/MappingUtils.java test/jalview/util/MappingUtilsTest.java

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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3806 JAL-3725 update tests since CDS mappings now exclude the stop codon

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    /test/jalview/io/EmblFlatFileTest.java
JAL-3806 require mapping extent covers both sequence’s dataset sequence to avoid spurious mappings from overlapping CDS

JAL-3949 upgraded log4j to 2.17.1 (no actual known vulnerabilities\!), though this doesn't fix the issue

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    /j11lib/log4j-1.2-api-2.17.1.jar
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    /j11lib/log4j-api-2.17.1.jar
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    /j11lib/log4j-core-2.17.1.jar
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    /j11lib/log4j-slf4j18-impl-2.17.0.jar
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    /j11lib/log4j-slf4j18-impl-2.17.1.jar
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    /j8lib/log4j-1.2-api-2.17.1.jar
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    /j8lib/log4j-api-2.17.1.jar
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    /j8lib/log4j-core-2.17.1.jar
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    /j8lib/log4j-slf4j18-impl-2.17.0.jar
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    /j8lib/log4j-slf4j18-impl-2.17.1.jar
JAL-3806 use the covers() test for each selected sequence and the complementary alignment’s sequence as a filter for direct CDS-Protein mappings (ensures overlapping CDS coding for distinct proteins do not all get selected)

JAL-3806 use same logic as for mouse over highlighting to work out extent of selected region in complement alignment

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    /src/jalview/util/MappingUtils.java
JAL-3806 todo - problem seems to be Protein:Many CDS are not selected

JAL-2305 comments re testFindXrefSequences_withFetch is failing - looks like test data needs to be revised for assumptions made by CrossRef about sequences retrieved from dbsources

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    /src/jalview/analysis/CrossRef.java
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    /test/jalview/analysis/CrossRefTest.java