jalview

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JAL-2491 Missed port to applet from JAL-1691

Merge branch 'documentation/JAL-2418_release2102' into develop

JAL-2418 updated JPred documentation and screenshot for JPred4

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    /help/html/webServices/jnet.html
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    /help/html/webServices/jnetprediction.gif
JAL-2418 JAL-2549 JABAWS 2.2 release notes

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    /help/html/webServices/msaclient.html
Merge branch 'features/JAL-2549_updateJABAWSto220' into develop

JAL-2465 Improvement to re-instate storing recently opened URLs for alignments loaded from a structure format via URL

JAL-2465 fix to prevent files loaded from the system's temporary directory from being included in recently opend files store

Merge branch 'features/JAL-1648_cache_user_inputs' of https://source.jalview.org/git/jalview into features/JAL-1648_cache_user_inputs

JAL-1648 fix to transfer focus back to alignment frame when Finder window is close via hitting cancel or the excape key

JAL-2290 no update if no change of residue JAL-2547 no features on tooltip over gap

JAL-2480 move ContiguousI and Range to jalview.datamodel

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    /src/jalview/datamodel/ContiguousI.java
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    /src/jalview/datamodel/Range.java
JAL-2557 removal of Sequence.sequenceFeatures

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    /src/jalview/analysis/CrossRef.java
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    /src/jalview/analysis/SeqsetUtils.java
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    /src/jalview/commands/EditCommand.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/gui/Jalview2XML.java
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    /src/jalview/io/vamsas/Datasetsequence.java
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    /test/jalview/analysis/AlignmentUtilsTests.java
  1. … 9 more files in changeset.
Merge branch 'develop' into features/JAL-1648_cache_user_inputs bugfixes in finder for feature creation and minimum window size merged to topic

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    /resources/lang/Messages.properties
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    /src/jalview/gui/AnnotationColumnChooser.java
JAl-2034 Ported to applet

JAL-2034 don't update overview after click without drag on group

JAL-2050 make SequenceFeature.score final, adjust constructor calls

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/commands/EditCommand.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
  1. … 13 more files in changeset.
JAL-2505 simplifying number of SequenceFeature constructors JAL-2060 constant for NO_SCORE defined in SequenceFeature

JAL-2505 removed SequenceFeature constructor JAL-1641 include description, otherDetails in feature roundtrip verification

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    /test/jalview/io/JSONFileTest.java
JAL-2490 test coverage of empty and null feature group in Jalview format export

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    /test/jalview/io/FeaturesFileTest.java
Merge branch 'bug/JAL-2551' into bug/JAL-2034contextchange

JAL-2505 make SequenceFeature type, begin, end, featureGroup final

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    /test/jalview/datamodel/SequenceTest.java
JAL-2506 relocate Uniprot binding classes, bind to UniprotFeature not SequenceFeature

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    /src/jalview/datamodel/UniprotEntry.java
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    /src/jalview/datamodel/UniprotFile.java
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    /src/jalview/datamodel/xdb/uniprot/UniprotEntry.java
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    /src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
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    /src/jalview/datamodel/xdb/uniprot/UniprotFile.java
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    /src/jalview/datamodel/xdb/uniprot/UniprotProteinName.java
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    /src/jalview/datamodel/xdb/uniprot/UniprotSequence.java
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    /src/jalview/ws/dbsources/Uniprot.java
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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-2505 remove setters for SequenceFeature.begin,end,type,featureGroup

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    /test/jalview/ext/ensembl/EnsemblCdsTest.java
JAL-2529 add object_type=cdna to EnsemblCdna parameters

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    /src/jalview/ext/ensembl/EnsemblCdna.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
Merge branch 'bug/JAL-2541cutWithFeatures' into features/JAL-2446NCList

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    /src/jalview/commands/EditCommand.java
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    /src/jalview/datamodel/Sequence.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-2505 JAL-2542 SequenceFeatures.shift() to shift all positional features

JAL-2551 Fix to group colouring when group extent is reduced

JAL-2542 correct adjustment of sequence features for flanking sequence

JAL-2034 Added isDefined flag to SequenceGroup

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/SequenceGroup.java
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    /test/jalview/gui/AlignViewportTest.java
JAL-2505 delete and readd modified feature after Cut or Paste

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    /src/jalview/commands/EditCommand.java