jalview

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Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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    /src/jalview/analysis/AlignmentSorter.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/appletgui/TitledPanel.java
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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/AlignViewport.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/JvSwingUtils.java
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    /src/jalview/gui/OverviewPanel.java
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JAL-3783 Reverting to using groovy-all-2.4.12-indy.jar to fix serious problem with Groovy console using shadowJar

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    /j11lib/groovy-cli-commons-2.5.7.jar
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    /j11lib/groovy-cli-picocli-2.5.7.jar
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    /j11lib/groovy-docgenerator-2.5.7.jar
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JAL-3628 Test for doubly saved single backup file scheme

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    /test/jalview/io/BackupFilesTest.java
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    /test/jalview/io/testProps_singlefilebackup.jvprops
Merge branch 'Jalview-JS/develop_j2s_v3_2_9_j11' into Jalview-JS/develop

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

JAL-3117 bring alignment to foreground on click on Overview

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

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

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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    /test/jalview/gui/AlignmentPanelTest.java
JAL-3785 set full title on automatically opened Overview windows

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

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

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

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

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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/develop/resources/channel.props
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    /utils/channels/jalviewjs-release
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    /utils/channels/jalviewjs/channel_gradle.properties
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    /utils/channels/jalviewjs/images/UoD_banner-28.png
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JAL-3775 JAL-3633 Make java.net.Authenticator code conditional on not being JalviewJS

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    /src/jalview/jbgui/GPreferences.java
JAL-3690 Let's enable web services (seriously this time)

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    /swingjs/ver/3.2.4/_j2sclasslist.txt
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JAL-3690 Web services and interactive workers somewhat working.

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    /swingjs/differences.txt
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JAL-3612 use _last_ drawn colour per feature type in Overview

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

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/3.2.9-j11/differences.txt
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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