jalview

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Commits this week: 10
Total Committers: 73
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Commits this week: 10

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Tuesday 02 Jun 2020
12:30 pm

Bob Hanson

helpful hints from Ben

Options
    • -0
    • +23
    /swingjs/README-JALVIEW
11:19 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3446 latest jmol zip from JAL-3253-applet (commit c28e0a1)

Options
    • binary
    /utils/jalviewjs/libjs/jmol-app.zip
11:00 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3446 fix broken test

Options
    • -5
    • +1
    /src/jalview/util/ColorUtils.java
    • -3
    • +3
    /test/jalview/util/ColorUtilsTest.java
4:32 am

Bob Hanson

Bob's gitignore addition

/build-site.xml

/buildcore.xml

/j11lib/intervalstore-v1.0.jar

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    • -0
    • +3
    /.gitignore
4:27 am

Bob Hanson

SO option true for Java (from Jalview-JS/develop)

Options
    • -104
    • +9
    /src/jalview/bin/Jalview.java
4:13 am

Bob Hanson

JAL-3626 from JAL-3253-applet Jalview.java

adds JalviewLite interface; removes deprecated AppletContext interface

Options
    • -2
    • +2
    /src/jalview/api/JalviewApp.java
    • -297
    • +490
    /src/jalview/bin/Jalview.java
    • -1
    • +1
    /src/jalview/gui/AlignFrame.java
    • -22
    • +38
    /src/jalview/gui/AlignViewport.java
    • -28
    • +62
    /src/jalview/gui/Preferences.java
4:10 am

Bob Hanson

JAL-3626 from JAL-3253-applet Cache applicationProperties made private

-- adds remove/setPropertyNoSave

Options
    • -0
    • +67
    /build-libjs.xml
    • -1
    • +1
    /test/jalview/analysis/FinderTest.java
    • -3
    • +3
    /test/jalview/ext/jmol/JmolParserTest.java
    • -1
    • +1
    /test/jalview/gui/AlignFrameTest.java
    • -7
    • +7
    /test/jalview/gui/AlignViewportTest.java
    • -1
    • +1
    /test/jalview/gui/AlignmentPanelTest.java
    • -5
    • +5
    /test/jalview/gui/AnnotationChooserTest.java
    • -5
    • +5
    /test/jalview/gui/AnnotationColumnChooserTest.java
    • -2
    • +2
    /test/jalview/gui/AnnotationRowFilterTest.java
    • -2
    • +2
    /test/jalview/gui/CalculationChooserTest.java
    • -5
    • +5
    /test/jalview/gui/FreeUpMemoryTest.java
    • -1
    • +1
    /test/jalview/gui/SeqCanvasTest.java
    • -8
    • +8
    /test/jalview/gui/SeqPanelTest.java
    • -2
    • +2
    /test/jalview/io/AnnotatedPDBFileInputTest.java
    • -9
    • +9
    /test/jalview/io/BackupFilesTest.java
  16. … 3 more files in changeset.
2:17 am

Bob Hanson

JAL-3253-applet removes references to JalviewLite interface

no longer any need to implement the Jalview methods as an interface that

is common to JalviewLite

Options
    • -55
    • +58
    /src/jalview/bin/Jalview.java
    • -59
    • +59
    /src/jalview/bin/JalviewAppLoader.java
    • -2
    • +643
    /src/jalview/bin/JalviewJSApi.java
    • -2
    • +2
    /src/jalview/gui/Preferences.java
1:34 am

Bob Hanson

JAL-3626 from JAL-3253-applet Cache applicationProperties made private

-- adds remove/setPropertyNoSave

Options
    • -13
    • +76
    /src/jalview/bin/Cache.java
    • -1
    • +1
    /src/jalview/gui/ColourMenuHelper.java
    • -1
    • +1
    /src/jalview/gui/LineartOptions.java
    • -66
    • +66
    /src/jalview/gui/Preferences.java
1:32 am

Bob Hanson

JAL-3626 from JAL-3253-applet web page embedding

Options
    • -45
    • +872
    /src/jalview/bin/Jalview.java
    • -0
    • +1500
    /src/jalview/bin/JalviewAppLoader.java
    • -7
    • +44
    /src/jalview/gui/AlignFrame.java
    • -3
    • +3
    /src/jalview/gui/Desktop.java
    • -30
    • +25
    /src/jalview/gui/OverviewPanel.java
    • -4
    • +10
    /src/jalview/gui/PCAPanel.java
    • -1
    • +7
    /src/jalview/io/FileLoader.java
    • -1
    • +3
    /src/jalview/jbgui/GAlignFrame.java
    • -1
    • +3
    /src/jalview/jbgui/GDesktop.java
    • -1
    • +2
    /src/jalview/jbgui/GPCAPanel.java
    • -1
    • +2
    /src/jalview/jbgui/GStructureViewer.java
    • -1
    • +2
    /src/jalview/jbgui/GTreePanel.java
    • -4
    • +4
    /src/jalview/project/Jalview2XML.java
    • -3
    • +11
    /src/jalview/viewmodel/OverviewDimensions.java
    • -2
    • +15
    /src/jalview/viewmodel/OverviewDimensionsHideHidden.java
    • -2
    • +16
    /src/jalview/viewmodel/OverviewDimensionsShowHidden.java
Monday 01 Jun 2020
11:37 pm

Bob Hanson

JAL-3626 from JAL-3253-applet JalviewLite scrollTo capability

Options
    • -0
    • +63
    /src/jalview/gui/AlignFrame.java
    • -0
    • +117
    /src/jalview/gui/AlignmentPanel.java
    • -0
    • +42
    /src/jalview/gui/SeqPanel.java
11:25 pm

Bob Hanson

JAL-3626 from JAL-3253-applet CalculationChooser

-- dissociated from panel for static access by JavaScript

Options
    • -29
    • +136
    /src/jalview/gui/CalculationChooser.java
    • -0
    • +2
    /src/jalview/gui/Preferences.java
11:18 pm

Bob Hanson

JAL-3626 from JAL-3253-applet StructureViewer/Chooser

-- disassociates viewer launch from chooser

-- for JavaScript interface

(sorry about JAL-3262 ref previously)

Options
    • -165
    • +72
    /src/jalview/gui/StructureChooser.java
    • -0
    • +117
    /src/jalview/gui/StructureViewer.java
10:48 pm

Bob Hanson

JAL-3262 from JAL-3253-applet temp. Desktop instance hack

Options
    • -0
    • +11
    /src/jalview/gui/Desktop.java
10:43 pm

Bob Hanson

JAL-3262 from JAL-3253-applet JalviewApp integration

Options
    • -0
    • +27
    /src/jalview/gui/AlignFrame.java
10:41 pm

Bob Hanson

JAL-3262 from JAL-3253-applet JalviewApp integration

Options
    • -5
    • +14
    /src/jalview/gui/AlignFrame.java
10:39 pm

Bob Hanson

JAL-3262 from JAL-3253-applet AppletParams + Cache.setPropertyNoSave

Options
    • -0
    • +447
    /src/jalview/bin/AppletParams.java
    • -0
    • +52
    /src/jalview/bin/Cache.java
10:33 pm

Bob Hanson

JAL-3262 from JAL-3253-applet ArgsParser

Options
    • -7
    • +94
    /src/jalview/bin/ArgsParser.java
10:29 pm

Bob Hanson

JAL-3262 from JAL-3253-applet Platform JS interface upgrade

Options
    • -0
    • +11
    /src/jalview/util/Platform.java
10:29 pm

Bob Hanson

JAL-3262 from JAL-3253-applet Preferences final static String upgrade

Options
    • -12
    • +108
    /src/jalview/gui/Preferences.java
10:20 pm

Bob Hanson

JAL-3262 from JAL-3523-applet JalviewApp and JalviewJSApi

- removes JaliewJSLite dependence

- removes AlignFrameI reference

Options
    • -0
    • +82
    /src/jalview/api/JalviewApp.java
    • -0
    • +693
    /src/jalview/bin/JalviewJSApi.java
10:14 pm

Bob Hanson

JAL-3262 from JAL3253-applet core_jvjmol.z.js static load

Options
    • -0
    • +11
    /src/jalview/gui/StructureViewer.java
10:10 pm

Bob Hanson

JAL-3626 Regex optimization from JAL-3253-applet; also minor StockholmFile for loop opt.

Options
    • -1
    • +2
    /src/jalview/analysis/Finder.java
    • -1
    • +2
    /src/jalview/analysis/ParseProperties.java
    • -1
    • +2
    /src/jalview/ext/ensembl/EnsemblCdna.java
    • -1
    • +1
    /src/jalview/ext/ensembl/EnsemblGene.java
    • -1
    • +2
    /src/jalview/ext/ensembl/EnsemblProtein.java
    • -1
    • +2
    /src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
    • -3
    • +12
    /src/jalview/io/ModellerDescription.java
    • -34
    • +102
    /src/jalview/io/NewickFile.java
    • -1
    • +2
    /src/jalview/io/RnamlFile.java
    • -83
    • +144
    /src/jalview/io/StockholmFile.java
    • -2
    • +10
    /src/jalview/util/DBRefUtils.java
    • -2
    • +5
    /src/jalview/util/Platform.java
    • -1
    • +8
    /src/jalview/ws/dbsources/EmblCdsSource.java
    • -1
    • +8
    /src/jalview/ws/dbsources/EmblSource.java
    • -1
    • +9
    /src/jalview/ws/dbsources/Pdb.java
    • -1
    • +10
    /src/jalview/ws/dbsources/Uniprot.java
8:22 pm

Bob Hanson

THIRDPARTYLIBS referred to intervalstore-v1.0 still

Options
    • -1
    • +1
    /THIRDPARTYLIBS
8:12 pm

Bob Hanson

corrects Platform.openURL

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    • -2
    • +0
    /src/jalview/util/Platform.java
8:02 pm

Bob Hanson

JAL-3626 adding compatible Platform.java

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    • -100
    • +285
    /src/jalview/util/Platform.java
6:40 pm

Bob Hanson

SwingJS update

Options
    • -0
    • +6
    /src/swingjs/api/js/README.txt
    • binary
    /swingjs/SwingJS-site.zip
    • binary
    /swingjs/net.sf.j2s.core-j11.jar
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9-j11/net.sf.j2s.core-j11.jar
    • -1
    • +1
    /swingjs/ver/3.2.9-j11/timestamp
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • -1
    • +1
    /swingjs/ver/3.2.9/timestamp
6:38 pm

Bob Hanson

Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

Options
6:32 pm

Bob Hanson

swingjs/api, javajs/async

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    • -0
    • +594
    /src/javajs/async/Assets.java
    • -0
    • +189
    /src/javajs/async/Async.java
    • -0
    • +67
    /src/javajs/async/AsyncColorChooser.java
    • -0
    • +282
    /src/javajs/async/AsyncDialog.java
    • -0
    • +217
    /src/javajs/async/AsyncFileChooser.java
    • -0
    • +385
    /src/javajs/async/AsyncSwingWorker.java
    • -0
    • +651
    /src/javajs/async/SwingJSUtils.java
    • -0
    • +78
    /src/swingjs/api/Interface.java
    • -0
    • +7
    /src/swingjs/api/JSFileHandler.java
    • -170
    • +317
    /src/swingjs/api/JSUtilI.java
    • -0
    • +309
    /src/swingjs/api/js/DOMNode.java
    • -0
    • +58
    /src/swingjs/api/js/HTML5AudioContext.java
    • -0
    • +59
    /src/swingjs/api/js/HTML5Canvas.java
    • -0
    • +164
    /src/swingjs/api/js/HTML5CanvasContext2D.java
    • -0
    • +7
    /src/swingjs/api/js/HTML5DataTransfer.java
  16. … 6 more files in changeset.
6:23 pm

Bob Hanson

JAL-3626 reconciled Platform

- replaces escapeString with escapeBackslashes

- adds pathEquals

Options
    • -2
    • +2
    /src/jalview/gui/AppJmol.java
    • -1
    • +1
    /src/jalview/gui/ChimeraViewFrame.java
    • -1
    • +2
    /src/jalview/project/Jalview2XML.java
    • -1
    • +3
    /src/jalview/structure/StructureSelectionManager.java
    • -14
    • +31
    /src/jalview/util/Platform.java