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Merge branch 'develop' into merged_2_11_2_0_to_2_12 updates JAL-3362 2.12 alpha with 2.11.2.5 release changes. Still has failing tests. Conflicts: THIRDPARTYLIBS build.gradle gradle.properties help/help/html/features/preferences.html help/help/html/releases.html src/jalview/bin/Cache.java src/jalview/bin/Jalview.java src/jalview/datamodel/SequenceI.java src/jalview/fts/service/uniprot/UniProtFTSRestClient.java src/jalview/gui/AlignFrame.java src/jalview/gui/AlignViewport.java src/jalview/gui/AlignmentPanel.java src/jalview/gui/AnnotationPanel.java src/jalview/gui/Desktop.java src/jalview/gui/FeatureEditor.java src/jalview/gui/IdCanvas.java src/jalview/gui/JvSwingUtils.java src/jalview/gui/OptsAndParamsPage.java src/jalview/gui/OverviewPanel.java src/jalview/gui/PopupMenu.java src/jalview/gui/Preferences.java src/jalview/gui/SeqCanvas.java src/jalview/gui/SeqPanel.java src/jalview/gui/SequenceFetcher.java src/jalview/gui/SplashScreen.java src/jalview/gui/SplitFrame.java src/jalview/gui/StructureChooser.java src/jalview/gui/UserQuestionnaireCheck.java src/jalview/gui/VamsasApplication.java src/jalview/gui/WsJobParameters.java src/jalview/gui/WsParamSetManager.java src/jalview/io/BackupFiles.java src/jalview/io/ModellerDescription.java src/jalview/io/NewickFile.java src/jalview/io/SequenceAnnotationReport.java src/jalview/io/StockholmFile.java src/jalview/javascript/log4j/Logger.java src/jalview/jbgui/GAlignFrame.java src/jalview/jbgui/GCutAndPasteHtmlTransfer.java src/jalview/jbgui/GCutAndPasteTransfer.java src/jalview/jbgui/GDesktop.java src/jalview/jbgui/GPreferences.java src/jalview/project/Jalview2XML.java src/jalview/structure/StructureSelectionManager.java src/jalview/urls/IdentifiersUrlProvider.java src/jalview/util/HttpUtils.java src/jalview/util/MappingUtils.java src/jalview/util/MessageManager.java src/jalview/util/Platform.java src/jalview/util/StringUtils.java src/jalview/viewmodel/AlignmentViewport.java src/jalview/ws/AWSThread.java src/jalview/ws/dbsources/EmblXmlSource.java src/jalview/ws/gui/MsaWSThread.java src/jalview/ws/jws1/Discoverer.java src/jalview/ws/jws2/AADisorderClient.java src/jalview/ws/jws2/AbstractJabaCalcWorker.java src/jalview/ws/jws2/Jws2Client.java src/jalview/ws/jws2/Jws2Discoverer.java src/jalview/ws/jws2/MsaWSClient.java src/jalview/ws/rest/HttpResultSet.java src/jalview/ws/rest/RestClient.java src/jalview/ws/rest/RestJobThread.java src/jalview/ws/utils/UrlDownloadClient.java src/jalview/xml/binding/jalview/DoubleVector.java src/jalview/xml/binding/jalview/JalviewModel.java test/jalview/bin/CommandLineOperations.java test/jalview/ext/jmol/JmolCommandsTest.java test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java test/jalview/gui/AlignViewportTest.java test/jalview/gui/AlignmentPanelTest.java test/jalview/gui/AnnotationChooserTest.java test/jalview/gui/AnnotationRowFilterTest.java test/jalview/gui/JvSwingUtilsTest.java test/jalview/gui/SeqCanvasTest.java test/jalview/gui/SequenceRendererTest.java test/jalview/gui/StructureChooserTest.java test/jalview/io/SequenceAnnotationReportTest.java test/jalview/project/Jalview2xmlTests.java test/jalview/renderer/OverviewResColourFinderTest.java test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java test/jalview/schemes/ClustalxColourSchemeTest.java test/jalview/structure/StructureSelectionManagerTest.java test/jalview/util/ColorUtilsTest.java test/jalview/workers/AlignCalcManagerTest.java test/jalview/ws/gui/Jws2ParamView.java test/jalview/ws/sifts/SiftsClientTest.java

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    ./seqfeatures/FeatureColourFinderTest.java
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    ./seqfeatures/FeatureRendererTest.java
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Merge branch 'bug/JAL-3612_overviewFeatureOrdering' into develop

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    ./seqfeatures/FeatureColourFinderTest.java
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JAL-3746 apply copyright to tests

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    ./seqfeatures/FeatureColourFinderTest.java
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JAL-3438 spotless for 2.11.2.0

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    ./OverviewResColourFinderTest.java
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    ./seqfeatures/FeatureColourFinderTest.java
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    ./seqfeatures/FeatureRendererTest.java
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JAL-3438 - all src and test run through spotless..

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    ./OverviewResColourFinderTest.java
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    ./seqfeatures/FeatureColourFinderTest.java
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    ./seqfeatures/FeatureRendererTest.java
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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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    ./seqfeatures/FeatureColourFinderTest.java
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JAL-3612 use _last_ drawn colour per feature type in Overview

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    ./seqfeatures/FeatureColourFinderTest.java
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JAL-1713 refactorings to allow save/restore Overview to/from project

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    ./OverviewResColourFinderTest.java
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JAL-3719 patch test for user colour scheme with/out gap color

JAL-3719 patch test for user colour scheme with/out gap color

JAL-3446 more tweaks to tests failing on build server

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    ./seqfeatures/FeatureColourFinderTest.java
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JAL-3446 tearDown to fix unit test fail

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    ./seqfeatures/FeatureRendererTest.java
I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha update for 2.11.1 release

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    ./seqfeatures/FeatureColourFinderTest.java
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JAL-3187 unit test for findComplementFeaturesAtResidue

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    ./seqfeatures/FeatureRendererTest.java
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JAL-32423 tidying

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    ./seqfeatures/FeatureColourFinderTest.java
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JAL-3442 colour caching for Overview resize

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JAL-3383 removing colour caching (to a separate branch)

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JAL-3383 minor code tidying and commenting

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I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit ...

I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit with the issue.

This reset also needs to happen in copyAlignPanel() (which also calls loadViewport() where the flag is set on).

This reset also needs to happen in copyAlignPanel() (which also calls loadViewport() where the flag is set on).

JAL-3253-applet JAL-3423 Windows TestNG

FeatureColourFinderTest error only in batch mode

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    ./seqfeatures/FeatureColourFinderTest.java
JAL-3210 Barebones gradle/buildship/eclipse. See README

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    ./OverviewResColourFinderTest.java
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    ./seqfeatures/FeatureColourFinderTest.java
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    ./seqfeatures/FeatureRendererTest.java
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JAL-3253-applet no-NCList IntervalStore fixes

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Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into merge-212

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    ./seqfeatures/FeatureColourFinderTest.java
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JAL-3369 JAL-3253-applet adds embedded dim checking for overview frame

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Can't reproduce this now (can't "bring desktop to front"). Will resolve and reopen if it recurs.

Can't reproduce this now (can't "bring desktop to front"). Will resolve and reopen if it recurs.