Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
Merge branch 'develop' into merged_2_11_2_0_to_2_12 updates JAL-3362 2.12 alpha with 2.11.2.5 release changes. Still has failing tests. Conflicts: THIRDPARTYLIBS build.gradle gradle.properties help/help/html/features/preferences.html help/help/html/releases.html src/jalview/bin/Cache.java src/jalview/bin/Jalview.java src/jalview/datamodel/SequenceI.java src/jalview/fts/service/uniprot/UniProtFTSRestClient.java src/jalview/gui/AlignFrame.java src/jalview/gui/AlignViewport.java src/jalview/gui/AlignmentPanel.java src/jalview/gui/AnnotationPanel.java src/jalview/gui/Desktop.java src/jalview/gui/FeatureEditor.java src/jalview/gui/IdCanvas.java src/jalview/gui/JvSwingUtils.java src/jalview/gui/OptsAndParamsPage.java src/jalview/gui/OverviewPanel.java src/jalview/gui/PopupMenu.java src/jalview/gui/Preferences.java src/jalview/gui/SeqCanvas.java src/jalview/gui/SeqPanel.java src/jalview/gui/SequenceFetcher.java src/jalview/gui/SplashScreen.java src/jalview/gui/SplitFrame.java src/jalview/gui/StructureChooser.java src/jalview/gui/UserQuestionnaireCheck.java src/jalview/gui/VamsasApplication.java src/jalview/gui/WsJobParameters.java src/jalview/gui/WsParamSetManager.java src/jalview/io/BackupFiles.java src/jalview/io/ModellerDescription.java src/jalview/io/NewickFile.java src/jalview/io/SequenceAnnotationReport.java src/jalview/io/StockholmFile.java src/jalview/javascript/log4j/Logger.java src/jalview/jbgui/GAlignFrame.java src/jalview/jbgui/GCutAndPasteHtmlTransfer.java src/jalview/jbgui/GCutAndPasteTransfer.java src/jalview/jbgui/GDesktop.java src/jalview/jbgui/GPreferences.java src/jalview/project/Jalview2XML.java src/jalview/structure/StructureSelectionManager.java src/jalview/urls/IdentifiersUrlProvider.java src/jalview/util/HttpUtils.java src/jalview/util/MappingUtils.java src/jalview/util/MessageManager.java src/jalview/util/Platform.java src/jalview/util/StringUtils.java src/jalview/viewmodel/AlignmentViewport.java src/jalview/ws/AWSThread.java src/jalview/ws/dbsources/EmblXmlSource.java src/jalview/ws/gui/MsaWSThread.java src/jalview/ws/jws1/Discoverer.java src/jalview/ws/jws2/AADisorderClient.java src/jalview/ws/jws2/AbstractJabaCalcWorker.java src/jalview/ws/jws2/Jws2Client.java src/jalview/ws/jws2/Jws2Discoverer.java src/jalview/ws/jws2/MsaWSClient.java src/jalview/ws/rest/HttpResultSet.java src/jalview/ws/rest/RestClient.java src/jalview/ws/rest/RestJobThread.java src/jalview/ws/utils/UrlDownloadClient.java src/jalview/xml/binding/jalview/DoubleVector.java src/jalview/xml/binding/jalview/JalviewModel.java test/jalview/bin/CommandLineOperations.java test/jalview/ext/jmol/JmolCommandsTest.java test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java test/jalview/gui/AlignViewportTest.java test/jalview/gui/AlignmentPanelTest.java test/jalview/gui/AnnotationChooserTest.java test/jalview/gui/AnnotationRowFilterTest.java test/jalview/gui/JvSwingUtilsTest.java test/jalview/gui/SeqCanvasTest.java test/jalview/gui/SequenceRendererTest.java test/jalview/gui/StructureChooserTest.java test/jalview/io/SequenceAnnotationReportTest.java test/jalview/project/Jalview2xmlTests.java test/jalview/renderer/OverviewResColourFinderTest.java test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java test/jalview/schemes/ClustalxColourSchemeTest.java test/jalview/structure/StructureSelectionManagerTest.java test/jalview/util/ColorUtilsTest.java test/jalview/workers/AlignCalcManagerTest.java test/jalview/ws/gui/Jws2ParamView.java test/jalview/ws/sifts/SiftsClientTest.java

  1. … 245 more files in changeset.
JAL-4028 experiment - THISISAPLACEHOLDER sequences get additional sequence data (as ‘X’) to cover the extent of features on the sequence.

  1. … 2 more files in changeset.
JAL-3438 spotless for 2.11.2.0

  1. … 655 more files in changeset.
JAL-3438 - all src and test run through spotless..

  1. … 662 more files in changeset.
JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

  1. … 101 more files in changeset.
Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work! Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this m...

Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work!
Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this method seems to be trying to do two different things.

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called). So what is it there for?

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called).
So what is it there for?

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

Needs proper Javadoc

Needs proper Javadoc

Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide...

Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide documentation.
e.g. http://source.jalview.org/gitweb/?p=jalview.git;a=blob;f=doc/JalviewJS-startupParams.md;h=9ff33529b2dbc2da34d2a573ccf5d042194fbb0d;hb=refs/heads/Jalview-JS/develop

Due to the number of changes this is likely to be a 'best efforts' review.

Due to the number of changes this is likely to be a 'best efforts' review.

Commits to JS-develop from 2nd to 25th June 2020
Commits to JS-develop from 2nd to 25th June 2020
JAL-3446 post-merge unit test fixes, formatting

  1. … 4 more files in changeset.
JAL-3664 support for user.home, user.dir, user

  1. … 12 more files in changeset.
JAL-3446 from JAL-3253 ApplicationSingletonProvider missing for RestClient; others are just cosmetic

  1. … 8 more files in changeset.
I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

JAL-3446 from JAL-3253 ApplicationSingletonProvider StructureSelectionManager and others

  1. … 24 more files in changeset.
JAL-3446 from JAL-3253 ApplicationSingletonProvider Desktop

  1. … 65 more files in changeset.
JAL-3621 corrected sequence feature sort and test

  1. … 1 more file in changeset.
JAL-3621 corrected sequence feature sort and test

  1. … 1 more file in changeset.
JAL-3621 corrected sequence feature sort and test

  1. … 1 more file in changeset.
Merge branch 'develop' into feature/JAL-3551Pymol

Conflicts:

src/jalview/ext/jmol/JalviewJmolBinding.java

src/jalview/ext/jmol/JmolCommands.java

src/jalview/gui/AppJmol.java

src/jalview/gui/AppJmolBinding.java

src/jalview/gui/ChimeraViewFrame.java

src/jalview/gui/StructureViewerBase.java

src/jalview/jbgui/GPreferences.java

src/jalview/jbgui/GStructureViewer.java

src/jalview/project/Jalview2XML.java

  1. … 19 more files in changeset.
JAL-3621 update to intervalstore v1.1

  1. … 4 more files in changeset.
JAL-3621 update to intervalstore v1.1

  1. … 4 more files in changeset.
JAL-3621 update to intervalstore v1.1

  1. … 4 more files in changeset.
Merge branch 'Jalview-JS/develop' into develop

Conflicts:

build.gradle

src/jalview/gui/PopupMenu.java

src/jalview/io/SequenceAnnotationReport.java

src/jalview/io/StockholmFile.java

src/jalview/util/DBRefUtils.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

  1. … 19 more files in changeset.

changeset discussion

  1. Jim Procter: relevant issue is JAL-3626