jalview

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

JAL-3594 Better Jalview Develop banner

JAL-3223 - update swingjs to 3.2.9-j11

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    /swingjs/ver/3.2.7/SwingJS-site.zip
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    /swingjs/ver/3.2.9-j11/differences.txt
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
JAL-3784 null the right overview reference when it is closed

JAL-1713 read/set OverviewPanel geometry on parent JInternalFrame

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    /src/jalview/project/Jalview2XML.java
JAL-1713 save Overview title in project, don't save Overview on New View

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    /src/jalview/project/Jalview2XML.java
JAL-3119 include view name (if any) in Overview title

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

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    /src/jalview/project/Jalview2XML.java
JAL-1713 refactorings to allow save/restore Overview to/from project

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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/OverviewResColourFinder.java
JAL-1713 schema and JAXB changes to save Overview in project file

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

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

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

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

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    /utils/channels/develop/images/jalview_develop_banner.xcf
JAL-3594 Images for splash screen

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    /resources/default_images/UoD_banner-28.png
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    /src/jalview/util/ChannelProperties.java
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JAL-3594 JAL-3728 Added taskbar icons to desktop and Java console. Changed "Jalview" to "app_name" in various appropriate places

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    /src/jalview/util/ChannelProperties.java
Merge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into merge/JAL-3594_and_new_develop_issues

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    /src/jalview/bin/Jalview.java
JAL-3594 Change main window title

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    /utils/install4j/README-DMG_creation.md
JAL-3594 DMG fixes

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    /utils/install4j/README-DMG_background_image_creation.md
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    /utils/install4j/README-DMG_creation.md
JAL-3594 added BG logo. Changed some named Jalviews to app_name property. Added test-release and default channels.

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    /src/jalview/util/ChannelProperties.java
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    /utils/channels/default/channel_gradle.properties
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JAL-3754 Fixed jar task creating strange dir because of outputs.file()

JAL-3754 Fixed jar task creating strange dir because of outputs.file()

Revert "JAL-3690 for a laugh, lets enable web services!"

This reverts commit 026057e76ba227a13968eb0ff3c01dc6b87145f4.

JAL-3690 update to swingjs patch 3.2.9

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    /swingjs/ver/3.2.7/SwingJS-site.zip
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    /swingjs/ver/3.2.9-j11/differences.txt
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    /swingjs/ver/3.2.9-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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JAL-3594 Default values for channel properties defined in code as fallback

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    /src/jalview/util/ChannelProperties.java
JAL-3739 catch parameter errors and report to the user

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    /resources/lang/Messages_es.properties
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    /src/jalview/ws/jws2/MsaWSClient.java
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    /src/jalview/ws/jws2/dm/JabaOption.java
JAL-3739 validate input on tab out of field

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    /src/jalview/gui/OptsAndParamsPage.java
JAL-3739 always take input values from form fields (not defaults)

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    /src/jalview/ws/jws2/Jws2Client.java
JAL-3739 use logger to reduce debug output

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    /src/jalview/gui/WsJobParameters.java
JAL-3594 Added rotating logo png

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    /src/jalview/gui/WebserviceInfo.java