jalview

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JAL-3789 Removed debugging printlns

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    /Java2ScriptCompilationParticipant.java
JAL-3789 First attempt for configurable property to look at

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    /Java2ScriptCompilationParticipant.java
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    /Java2ScriptCompiler.java
JAL-1713 restore project with no Overview, regardless of Preferences

JAL-3690 recoded AWSThread to use javax.swing.Timer (see https://github.com/BobHanson/java2script/issues/195#issuecomment-747695834 )- web service submission works, but doesn’t seem to be happening as a background task.

JAL-1713 close and replace auto-opened Overview with restored Overview

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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/project/Jalview2XML.java
JAL-3690 patch out use of java.streams/spliterator not supported in java2script (yet)

JAL-3690 tweak J2S direct DB access registration for jalview, compbio and other sites

JAL-3690 direct access to slivka, compbio, jalview.org and localhost/loopback.

JAL-3690 patch out need for java.time in j2s (see https://github.com/BobHanson/java2script/issues/194 )

JAL-3690 patch out spinning animation for web service jobs

JAL-3690 disable proxy server for JalviewJS

JAL-3280 Fixed the version checking URL formulation (getdown build_properties) for jalviewjs, can also use it for jalviewjs in future

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-all-2.4.12-indy.jar
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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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    /utils/channels/jalviewjs/images/UoD_banner-32.png
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    /utils/channels/jalviewjs/images/barton_group-30.png
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    /utils/channels/jalviewjs/images/barton_group-512.png
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    /utils/channels/jalviewjs/images/barton_group-62.png
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    /utils/channels/jalviewjs/images/barton_group-white-512.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/SwingJS-site.zip
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    /swingjs/ver/3.2.4/_j2sclasslist.txt
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
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JAL-3690 Web services and interactive workers somewhat working.

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    /swingjs/differences.txt
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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/_j2sclasslist.txt
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
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JAL-3612 use _last_ drawn colour per feature type in Overview