jalview

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Commits this week: 2
Total Committers: 72
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Commits this week: 2

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Thursday 09 Apr 2020
11:54 am

Ben Soares

JAL-3289 New getdown splashscreens to be used with different getdown channels

Options
    • binary
    /utils/getdown/jalview_logo_background_fade-640x480.xcf
    • binary
    /utils/getdown/jalview_logo_background_getdown-ARCHIVE-640x480.png
    • binary
    /utils/getdown/jalview_logo_background_getdown-BUILD-640x480.png
    • binary
    /utils/getdown/jalview_logo_background_getdown-DEVELOP-640x480.png
    • binary
    /utils/getdown/jalview_logo_background_getdown-LOCAL-640x480.png
    • binary
    /utils/getdown/jalview_logo_background_getdown-NON-RELEASE-640x480.png

changeset discussion

  1. Jim Procter: Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?
  2. Ben Soares: Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created w...
Wednesday 08 Apr 2020
8:32 pm

Bob Hanson

reconciled with applet

Options
    • -4
    • +4
    /src/jalview/io/BackupFiles.java
    • -9
    • +9
    /test/jalview/io/BackupFilesTest.java
8:32 pm

Bob Hanson

reconciled with develop

Options
    • -8
    • +8
    /src/jalview/gui/FeatureTypeSettings.java
    • -5
    • +4
    /src/jalview/io/BackupFilenameParts.java
    • -29
    • +39
    /test/jalview/io/BackupFilesTest.java
8:17 pm

Bob Hanson

comments only

Options
    • -1
    • +1
    /src/jalview/project/Jalview2XML.java
    • -1
    • +1
    /src/jalview/ws/jws2/SequenceAnnotationWSClient.java
8:16 pm

Bob Hanson

reconciled with applet

Options
    • -0
    • +155
    /src/jalview/bin/ApplicationSingletonProvider.java
    • -111
    • +302
    /src/jalview/bin/Cache.java
    • -169
    • +345
    /src/jalview/gui/Preferences.java
    • -4
    • +4
    /src/jalview/io/BackupFiles.java
    • -11
    • +45
    /src/jalview/jbgui/GPreferences.java
8:15 pm

Bob Hanson

3253 reconciled with develop

Options
    • -141
    • +271
    /src/jalview/bin/Cache.java
    • -17
    • +6
    /src/jalview/gui/JvSwingUtils.java
    • -88
    • +104
    /src/jalview/gui/Preferences.java
    • -32
    • +11
    /src/jalview/io/BackupFiles.java
    • -0
    • +173
    /src/jalview/io/BackupFilesPresetEntry.java
    • -0
    • +21
    /src/jalview/io/IntKeyStringValueEntry.java
    • -3
    • +6
    /src/jalview/io/PIRFile.java
    • -216
    • +257
    /src/jalview/jbgui/GPreferences.java
4:08 pm

Bob Hanson

JAL-3253 Platform reconciled with applet

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    • -118
    • +328
    /src/jalview/util/Platform.java
4:05 pm

Bob Hanson

JAL-3253 reconciled with Jalview-JS/develop (cosmetic changes)

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    • -20
    • +27
    /src/jalview/util/Platform.java
4:00 pm

Bob Hanson

JAL-3253 reconciled with Jalview-JS/develop

Options
    • -56
    • +102
    /src/jalview/util/Platform.java
3:25 pm

Bob Hanson

JAL-3253 removing old .cvsIgnore not in develop

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    • -1
    • +0
    /src/jalview/.cvsignore
    • -3
    • +0
    /src/jalview/analysis/.cvsignore
    • -5
    • +0
    /src/jalview/datamodel/.cvsignore
    • -11
    • +0
    /src/jalview/gui/.cvsignore
    • -2
    • +0
    /src/jalview/io/.cvsignore
    • -3
    • +0
    /src/jalview/jbgui/.cvsignore
    • -1
    • +0
    /src/jalview/util/.cvsignore
    • -3
    • +0
    /src/jalview/ws/.cvsignore
    • -1
    • +0
    /src/mc_view/.cvsignore
3:12 pm

Bob Hanson

JAL-3253 SwingJS upgrade including J11 transpiler 3.2.9.v1f

Options
    • binary
    /swingjs/SwingJS-site.zip
    • -1
    • +0
    /swingjs/_j2sclasslist.txt
    • binary
    /swingjs/net.sf.j2s.core-j11.jar
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /swingjs/ver/3.2.9/_j2sclasslist.txt
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    /swingjs/ver/3.2.9/net.sf.j2s.core-j11.jar
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/ver/3.2.9/timestamp
3:12 pm

Bob Hanson

JAL-3253 merge of new SwingJS api

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    • -0
    • +185
    /src/swingjs/api/JSUtilI.java
    • -0
    • +35
    /src/swingjs/api/js/HTML5Applet.java
2:50 pm

Bob Hanson

JAL-3585 Focus lost when closing menu -- SwingJS-siste.zip only

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    • binary
    /swingjs/SwingJS-site.zip
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • -1
    • +1
    /swingjs/ver/3.2.9/timestamp
2:25 pm

Ben Soares

JAL-3588 Auto insert of Examples folder into DMG and an attempt to style both the Volume icon and the Examples folder icon (icons not working)

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    • -2
    • +40
    /build.gradle
    • -1
    • +4
    /gradle.properties
    • binary
    /utils/install4j/DMG.VolumeIcon.icns
    • binary
    /utils/install4j/DS_Store
    • binary
    /utils/install4j/examples_folder.png
    • -2
    • +4
    /utils/install4j/install4j8_template.install4j
    • -0
    • +0
    /utils/install4j/jalview_macos_examples_folder_icon
Tuesday 07 Apr 2020
11:31 pm

Bob Hanson

JAL-3588 DnD fails; JAL-3587 Jalview project file loading fails

SwingJS fixes:

- DropTarget should access Component.peer directly, not via getPeer()

- Fast JavaScript Map must switch to slow Java Map when any key is

checked that is not a string literal.

Options
    • binary
    /swingjs/SwingJS-site.zip
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/ver/3.2.9/timestamp
11:31 pm

Bob Hanson

JAL-3253

sets setting for "unlikely argument type for collection" to warning; I

have set my workspace to error, but clearly it had not been like that,

because it found three errors. But now setting it to warning so that it

is not bothering me.

Options
    • -0
    • +5
    /.settings/org.eclipse.jdt.core.prefs
11:25 pm

Bob Hanson

JAL-3592 logic question

Options
    • -0
    • +7
    /src/jalview/viewmodel/AlignmentViewport.java
11:17 pm

Bob Hanson

JAL 3591 simple coding error in appletgui/SeqPanel

Options
    • -1
    • +2
    /src/jalview/appletgui/SeqPanel.java
8:39 pm

Ben Soares

merge from develop: the fixy bit

Options
    • -2
    • +0
    /build.gradle
8:14 pm

Ben Soares

merge from develop: the rest of the changes

Options
    • -6
    • +118
    /build.gradle
    • -7
    • +5
    /gradle.properties
5:55 pm

Ben Soares

merge from develop: Most of the changes

Options
    • -1
    • +1
    /src/jalview/gui/Desktop.java
4:27 pm

Bob Hanson

JAL-3589 (old Platform) fix for Jalvew-JS/develop only.

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    • -10
    • +9
    /src/jalview/util/Platform.java
2:30 pm

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

JAL-3210 fudge for JalviewJS to avoid IntervalStore incompatibility

Options
    • -8
    • +8
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
    • -16
    • +25
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
2:24 pm

Ben Soares

JAL-3577 improvement to non-release DMG background and source SVG. Updated docs on image specification/creation.

Options
    • -2
    • +6
    /utils/install4j/DMG_background_image_creation_README.md
    • binary
    /utils/install4j/jalview_dmg_background-NON-RELEASE.png
    • -215
    • +0
    /utils/install4j/jalview_dmg_background-NON-RELEASE.svg
    • -0
    • +44379
    /utils/install4j/jalview_dmg_background_blur_layers-NON-RELEASE.svg
12:48 pm

Jim Procter

Merge branch 'bug/JAL-247autoIdWidthSeqMarker' into develop

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    • -3
    • +3
    /src/jalview/gui/AlignmentPanel.java
    • -23
    • +26
    /src/jalview/gui/IdCanvas.java
1:30 am

Ben Soares

Merge branch 'task/JAL-3577_Jalview_Test_installers' into develop

Options
1:29 am

Ben Soares

JAL-3577 Added DEVELOP DMG styling. Improved TEST-RELEASE and NON-RELEASE styling

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    • -2
    • +5
    /build.gradle
    • binary
    /utils/install4j/DS_Store-DEVELOP
    • binary
    /utils/install4j/DS_Store-NON-RELEASE
    • -1
    • +1
    /utils/install4j/install4j8_template.install4j
    • binary
    /utils/install4j/jalview_dmg_background-DEVELOP.png
    • binary
    /utils/install4j/jalview_dmg_background-NON-RELEASE.png
    • binary
    /utils/install4j/jalview_dmg_background-TEST.png
Monday 06 Apr 2020
10:34 pm

Ben Soares

JAL-3577 Fixed Jalview Programme Group in Windows menu. Added examples folder for RELEASE channel only and Examples folder in Jalview Programme Group in Windows.

Options
    • -1
    • +31
    /build.gradle
    • -5
    • +27
    /utils/install4j/install4j8_template.install4j
5:48 pm

Jim Procter

Merge branch 'develop' into releases/Release_2_11_1_Branch

Options
5:47 pm

Jim Procter

JAL-3407 redact java 8 incompatible type inference

Options
    • -1
    • +1
    /src/jalview/gui/Desktop.java