jalview

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

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Monday 14 Dec 2020
4:12 pm

Ben Soares

JAL-3594 Allow setting of getdownappbase and getdowndistdir properties for DEVELOP channel, and change DEVELOP version to be VERSION-dDATE instead of VERSION-develop. dDATE will help users know when Jalview Develop applicaiton updated

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    • -7
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    /build.gradle
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    /src/jalview/bin/Cache.java
2:43 am

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

JAL-3117 bring alignment to foreground on click on Overview

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    /src/jalview/gui/AlignFrame.java
Sunday 13 Dec 2020
12:32 pm

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

JAL-1713 unit test for save/restore Overview in project

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    /test/jalview/project/Jalview2xmlTests.java
11:47 am

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

JAL-1713 renamed method to OverviewPanel.get/setFrameBounds()

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    /src/jalview/gui/OverviewPanel.java
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    /src/jalview/project/Jalview2XML.java
Saturday 12 Dec 2020
2:39 pm

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

JAL-1713 JAL-3119 JAL-3785 refactored get/set Overview bounds and title

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/OverviewPanel.java
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    /src/jalview/io/FileLoader.java
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    /src/jalview/project/Jalview2XML.java
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    /test/jalview/gui/AlignmentPanelTest.java
Friday 11 Dec 2020
9:04 pm

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

JAL-3785 set full title on automatically opened Overview windows

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    • -8
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/io/FileLoader.java
8:27 pm

Ben Soares

JAL-3594 Defintely want SplashScreen to appear in the Desktop window otherwise it might not be closeable

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    • -2
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    /src/jalview/gui/SplashScreen.java
5:19 pm

Ben Soares

JAL-3594 Changed building.md to describe -PCHANNEL=JALVIEWJS and JALVIEWJS-TEST

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    /doc/building.md
5:14 pm

Ben Soares

JAL-3594 Changed building.md to reflect change of name of channel_properties to channel.props

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    /doc/building.md
5:02 pm

Ben Soares

JAL-3594 Adjustments to allow JalviewJS to use ChannelProperties, and new utils/channels dir for jalviewjs and jalviewjs-release

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    /build.gradle
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    /src/jalview/gui/SplashScreen.java
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    /src/jalview/util/ChannelProperties.java
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    /utils/channels/default/resources/channel.props
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    /utils/channels/default/resources/channel_properties
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    /utils/channels/develop/resources/channel.props
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    /utils/channels/develop/resources/channel_properties
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    /utils/channels/jalviewjs-release
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    /utils/channels/jalviewjs/channel_gradle.properties
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  16. … 36 more files in changeset.
4:34 pm

Ben Soares

JAL-3775 JAL-3633 Make java.net.Authenticator code conditional on not being JalviewJS

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    • -65
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    /src/jalview/bin/Cache.java
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    /src/jalview/jbgui/GPreferences.java
2:33 pm

Mateusz Warowny

JAL-3690 Let's enable web services (seriously this time)

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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /swingjs/README.txt
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    /swingjs/ver/3.2.4/DEV_NOTES.txt
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    /swingjs/ver/3.2.4/_j2sclasslist.txt
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  16. … 27 more files in changeset.
2:33 pm

Mateusz Warowny

JAL-3690 Web services and interactive workers somewhat working.

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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /swingjs/ver/3.2.4/_j2sclasslist.txt
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  16. … 27 more files in changeset.
12:44 pm

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

JAL-3612 use _last_ drawn colour per feature type in Overview

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    • -1
    • +6
    /src/jalview/renderer/seqfeatures/FeatureRenderer.java
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    /test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
7:51 am

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

JAL-1713 fix typo; overview in project with open overview in preferences

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    • -5
    • +4
    /src/jalview/gui/AlignFrame.java
    • -1
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    /src/jalview/renderer/OverviewResColourFinder.java
Thursday 10 Dec 2020
7:56 pm

Ben Soares

Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop

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7:53 pm

Ben Soares

JAL-3594 Better Jalview Develop banner

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    /utils/channels/test-release/resources/channel_properties
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    /utils/channels/test-release/resources/images/jalview_banner.png
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    /utils/channels/test-release/resources/images/jalview_test-release_banner.png
5:50 pm

Jim Procter

JAL-3223 - update swingjs to 3.2.9-j11

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    /swingjs/differences.txt
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4:08 pm

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

JAL-3784 null the right overview reference when it is closed

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    • -1
    • +2
    /src/jalview/gui/AlignFrame.java
4:01 pm

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

JAL-1713 read/set OverviewPanel geometry on parent JInternalFrame

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    • +8
    /src/jalview/project/Jalview2XML.java
3:53 pm

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

JAL-1713 save Overview title in project, don't save Overview on New View

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    /schemas/jalview.xsd
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    /src/jalview/project/Jalview2XML.java
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    /src/jalview/xml/binding/jalview/JalviewModel.java
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    /src/jalview/xml/binding/jalview/package-info.java
2:56 pm

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

JAL-3119 include view name (if any) in Overview title

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    • -2
    • +8
    /src/jalview/gui/AlignFrame.java
1:05 pm

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

JAL-1713 save/restore Overview in project (todo: restore geometry)

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    /src/jalview/project/Jalview2XML.java
1:04 pm

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

JAL-1713 refactorings to allow save/restore Overview to/from project

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/OverviewCanvas.java
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    /src/jalview/gui/OverviewPanel.java
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    /src/jalview/gui/Preferences.java
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    /src/jalview/renderer/OverviewRenderer.java
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    /src/jalview/renderer/OverviewResColourFinder.java
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    /test/jalview/renderer/OverviewRendererTest.java
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    /test/jalview/renderer/OverviewResColourFinderTest.java
1:02 pm

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

JAL-1713 schema and JAXB changes to save Overview in project file

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    /schemas/jalview.xsd
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    /src/jalview/xml/binding/jalview/JalviewModel.java
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    /src/jalview/xml/binding/jalview/ObjectFactory.java
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    /src/jalview/xml/binding/jalview/package-info.java
10:49 am

Ben Soares

JAL-3594 Documentation added to building.md for using the utils/channels/... folders

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    /doc/building.md
10:05 am

Ben Soares

Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop

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9:56 am

Ben Soares

Merge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into develop

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    /build.gradle
Wednesday 09 Dec 2020
8:21 pm

Ben Soares

JAL-3594 Improved About banners for develop and test-release

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6:23 pm

Ben Soares

JAL-3594 Images for splash screen

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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/SplashScreen.java
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    /src/jalview/util/ChannelProperties.java
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  16. … 51 more files in changeset.