project

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-1713 restore project with no Overview, regardless of Preferences

  1. … 1 more file in changeset.
JAL-1713 close and replace auto-opened Overview with restored Overview

  1. … 3 more files in changeset.
Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

  1. … 56 more files in changeset.
JAL-1713 unit test for save/restore Overview in project

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 more tweaks to tests failing on build server

  1. … 2 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 Desktop

  1. … 66 more files in changeset.
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/AlignViewportI.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceI.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/JvSwingUtils.java

src/jalview/gui/OverviewPanel.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SplitFrame.java

src/jalview/gui/WsJobParameters.java

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/FileLoader.java

src/jalview/io/StockholmFile.java

src/jalview/jbgui/GAlignFrame.java

src/jalview/jbgui/GPreferences.java

src/jalview/renderer/AnnotationRenderer.java

src/jalview/viewmodel/AlignmentViewport.java

src/jalview/ws/jws2/Jws2Discoverer.java

test/jalview/analysis/AAFrequencyTest.java

test/jalview/gui/AlignFrameTest.java

test/jalview/gui/AlignViewportTest.java

  1. … 74 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
Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha update for 2.11.1 release

  1. … 42 more files in changeset.
JAL-3574 patch for Filters on genomic location
JAL-3574 patch for Filters on genomic location
JAL-3574 Matcher with integer/long value pattern (e.g. VCF POS locus)

  1. … 6 more files in changeset.
temp push

  1. … 128 more files in changeset.
JAL-3210 test updated for changed signature of SequenceI.getDBRefs()

JAL-3253 temporary branch SwingJS upgrade with testNG fixes Java 8

  1. … 51 more files in changeset.
JAL-3563 for merging to JAL-3253-applet

  1. … 1 more file in changeset.
classpath ordering

- j11lib needs to be declared before j8lib for saaj and probably many

others.

- Jalview.java allows synchronization

- CommandLineOperations working; seems at least on Bob's machine process

with file writing termination does not equate with file.exists(); join

is returning too early? How can that be...

- Jalview2xmlTests back to correct answer and now working with

Jalview.setSynchronized(true);

  1. … 4 more files in changeset.