jalview

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I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace. This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses...

I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace.
This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses. I notice that the new API server is sending back a 400 for bad input (including for non-existent query fields and wrong types for non-string query fields), which is invoking the warning triangle which puts the HTTP error message into the tooltip so this block is now getting more use!

The reason for wanting a full stacktrace in debug mode is that both the API and the changed client are new, so any errors in the next few months will be more quickly diagnosed if we can allow the user to easily obtain a stacktrace of the exception.

after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a con...

after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a convenient [search] button is shown so one doesn't have to click into the query field and press enter to trigger the search again.

should be Console.warn

should be Console.warn

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalvi...

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalview still work (up until legacy.uniprot.org goes away).

shouldn't this be a warn ?

shouldn't this be a warn ?

this comment block should really be after the imports ?

this comment block should really be after the imports ?

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API
JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API
JAL-1953 fix test and expected for canonical name for PFAM!

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    /test/jalview/util/DBRefUtilsTest.java
JAL-1953 update canonical db test for PFAM canonical name - also note could do the same for JAL-4022

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    /test/jalview/util/DBRefUtilsTest.java
JAL-1953 JAL-2889 don’t read additional lines when looking for phyloxml header

JAL-4021 todo & fix FileFormat tests

JAL-1953 2.11.2 with Archeopteryx! Minimal patches and Merge branch 'kjvdh/features/PhylogenyViewer' into merge/2_11_2/PhylogenyViewer also restored last kjvdh build of forester to j8 and j11lib directories Conflicts: .classpath j8lib/forester.jar resources/lang/Messages.properties src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java src/jalview/fts/core/GFTSPanel.java src/jalview/fts/service/pdb/PDBFTSPanel.java src/jalview/gui/AlignFrame.java src/jalview/gui/DasSourceBrowser.java src/jalview/gui/Desktop.java src/jalview/gui/PopupMenu.java src/jalview/gui/SplashScreen.java src/jalview/gui/StructureViewerBase.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/FileLoader.java src/jalview/io/HtmlSvgOutput.java src/jalview/project/Jalview2XML.java src/jalview/schemabinding/version2/JalviewModelSequence.java src/jalview/util/DBRefUtils.java src/jalview/viewmodel/AlignmentViewport.java src/jalview/ws/DBRefFetcher.java src/jalview/ws/DasSequenceFeatureFetcher.java src/jalview/ws/jws2/Jws2Discoverer.java utils/jalviewjs/buildxml/build.xml

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    /resources/lang/Messages.properties
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    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/ext/archaeopteryx/AptxFrame.java
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    /src/jalview/ext/treeviewer/JalviewBinding.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/CalculationChooser.java
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Revert "JAL-2799 all tabs now get mouse listeners and Jalview switches tree view"

This reverts commit 62f2ed464010270830afcfe954647a51dfb5114b.

minimal fixes - probably not valid since forester jar out of sync

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    /j11lib/forester.jar
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    /src/jalview/gui/AlignFrame.java
Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh/features/PhylogenyViewer_tabbedsupport Update from Release 2.11.2 develop branch JAL-1953 Conflicts: .classpath .project resources/lang/Messages.properties src/jalview/bin/Jalview.java src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java src/jalview/fts/core/GFTSPanel.java src/jalview/fts/service/pdb/PDBFTSPanel.java src/jalview/gui/AlignFrame.java src/jalview/gui/CalculationChooser.java src/jalview/gui/DasSourceBrowser.java src/jalview/gui/Desktop.java src/jalview/gui/PopupMenu.java src/jalview/gui/SplashScreen.java src/jalview/gui/StructureViewerBase.java src/jalview/gui/TreePanel.java src/jalview/gui/WebserviceInfo.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/FileLoader.java src/jalview/io/HtmlSvgOutput.java src/jalview/io/NewickFile.java src/jalview/math/Matrix.java src/jalview/math/MatrixI.java src/jalview/util/MappingUtils.java src/jalview/ws/DBRefFetcher.java src/jalview/ws/DasSequenceFeatureFetcher.java src/jalview/ws/jws2/Jws2Discoverer.java utils/eclipse/org.eclipse.jdt.core.jalview.prefs utils/eclipse/org.eclipse.jdt.ui.prefs

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    /src/jalview/analysis/TreeModel.java
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    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/ChimeraViewFrame.java
  1. … 24 more files in changeset.
Merge branch 'patch/JAL-4008_jabaws_2_2_1_patch' into doc/release_2_11_2_3

JAL-4012 JAL-4008 release notes for Jalview 2.11.2.3

JAL-4008 update jabaws client to 2.2.1 - definitely no log4j references !

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    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
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    /j11lib/jabaws-min-client-NO_LOG4J-2.2.1.jar
    • binary
    /j8lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j8lib/jabaws-min-client-NO_LOG4J-2.2.1.jar
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3992 bump version and report updates in 2.11.2.2 release notes

Merge branch 'bug/JAL-3997_NPE_in_wrapped_mode' into develop

Merge branch 'bug/JAL-3365_extendedDSSP_via_stockholm' into develop

JAL-3997 check for tooltip being null before checking equivalence to last tooltip string

Merge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm

JAL-3992 fix path

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    /help/help/html/features/cursorMode.html
JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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    /test/jalview/io/StockholmFileTest.java
JAL-3992 shift+arrow to jump to next gap/residue in cursor/keyboard editing mode

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    /help/help/html/features/cursorMode.html
Merge branch 'develop' into releases/Release_2_11_2_Branch