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Merge branch 'feature/JAL-3982_mouseover_highlighting_viaJAL-3860' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

JAL-3851 comment out some debugging

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-3851 Some streamlining of caching/removing from cache. 'Highlighting' in InputAlignment endpoint windows

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    /src/jalview/gui/CutAndPasteTransfer.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/InputAlignmentEndpoint.java
JAL-3851 Add a redirect back to itself for working endpoints

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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
Merge branch 'feature/JAL-3982_mouseover_highlighting_viaJAL-3860' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

JAL-3851 Allow specifying a sequence index in highlight

JAL-3982 highlight any 3D structure mappings for positions mapped via CDS/transcript relationships

JAL-3851 allow multiple instances of Endpoints. Fixes to naming of IGV colour scheme

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/CutAndPasteTransfer.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/InputAlignmentEndpoint.java
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    /src/jalview/rest/RestHandler.java
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    /src/jalview/schemes/IGVColourScheme.java
Merge branch 'ben/gecos_colour_schemes' into feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop

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
  1. … 3 more files in changeset.
Merge branch 'develop' into ben/gecos_colour_schemes

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
  1. … 59 more files in changeset.
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
  1. … 31 more files in changeset.
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
  1. … 647 more files in changeset.
JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes