jalview

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make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3982 todo notes

JAL-3860 prototype for highlight species/assembly/chromosome/position

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    /src/jalview/rest/HighlightGenomicRangeEndpoint.java
JAL-3982 JAL-3860 encapsulate genomic coordinates mapping/liftover logic

JAL-3860 JAL-3892 extract genomic assembly mapping logic to static store

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    /src/jalview/datamodel/GenomicAssemblies.java
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    /src/jalview/io/vcf/VCFLoader.java
JAL-3982 highlight any 3D structure mappings for positions mapped via CDS/transcript relationships

JAL-3851 Fix getRequestBody()

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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/InputAlignmentEndpoint.java
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    /src/jalview/rest/RestHandler.java
Merge branch 'feature/JAL-3851_rest_api_for_genome_browser' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

JAL-3851 merged to develop 2022-03-22

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    /doc/api_specification.md
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/SequenceFetcher.java
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    /src/jalview/httpserver/HttpServer.java
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    /src/jalview/rest/API.java
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    /src/jalview/rest/AbstractEndpoint.java
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    /src/jalview/rest/AbstractEndpointAsync.java
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    /src/jalview/rest/FetchSequencesEndpoint.java
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    /src/jalview/rest/GetCrossReferencesEndpoint.java
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    /src/jalview/rest/HighlightSequenceEndpoint.java
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    /src/jalview/rest/InputAlignmentEndpoint.java
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    /src/jalview/rest/RestHandler.java
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JAL-3746 bump release date to 10th March - after UoD network maintenance

JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(

JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert

JAL-3746 JAL-3841 fix README typo

JAL-3746 more docs tweaking and release notes

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    /help/help/html/features/preferences.html
Merge branch 'spike/try_spotless_JAL-3438' into develop

JAL-3746 apply copyright to tests

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    /test/jalview/bin/HiDPISettingTest1.java
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JAL-3746 apply copyright to source

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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/ext/rbvi/chimera/ChimeraXManager.java
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    /src/jalview/fts/api/StructureFTSRestClientI.java
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    /src/jalview/fts/service/threedbeacons/.gitignore
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    /src/jalview/gui/ChimeraXViewFrame.java
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JAL-3438 spotless for 2.11.2.0

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    /src/com/stevesoft/pat/ChangeRule.java
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    /src/com/stevesoft/pat/Ctrl.java
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    /src/com/stevesoft/pat/FastBracket.java
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    /src/com/stevesoft/pat/Regex.java
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    /src/com/stevesoft/pat/RegexWriter.java
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JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes

JAL-3108 updated Ensembl client and model species names

JAL-3746 new release date for 2.11.2

JAL-3746 JAL-3103 java.awt.Desktop.showURL method mechanism release notes

Merge branch 'bug/JAL-3103_browser_launcher_problems_macos_and_linux' into develop

JAL-3103 updated help doc to remove default browser choice

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    /help/help/html/features/preferences.html
JAL-3103 Removed code and unused widgets for defaultBrowser

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    /src/jalview/jbgui/GPreferences.java
JAL-3103 Remove BrowserLauncher2 and use Desktop.browse(url) with wrapper methods

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    /resources/lang/Messages_es.properties
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    /src/jalview/util/BrowserLauncher.java
JAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS

JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-needed exception handling from jalview code for openURL. Change Default browser input to JComboBox populated by BrowserLauncher2

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/jbgui/GPreferences.java
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    /src/jalview/util/BrowserLauncher.java