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JAL-2136 JAL-2137 Improvements: enable STRUCTMODEL annotation statement to be less stringent and backwards compatible, Link query and template sequences, transfer annotation from model to template sequence

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    /src/jalview/io/AnnotationFile.java
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    /src/jalview/ws/phyre2/Phyre2Client.java
JAL-2136 JAL-2137 Improved STRUCTMODEL annotation syntax to reinstated fasta file specification, improved implementation to link the Fasta mapping file to Phyre2 model entry, and moved Phyre2 model info from sequence detail to PDBEntry properties

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/io/AnnotationFile.java
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    /src/jalview/ws/phyre2/Phyre2Client.java
JAL-2136 JAL-2137 Modified STRUCTMODEL annotation format and added implementation to register Phyre2 model file from AnnotationFile such that it could be properly processed Phyre2 client on structure viewing.

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/io/AnnotationFile.java
JAL-2136 added improvement to parse crudelist file instead of scrapping 'summary.html' and renamed testfiles accordingly

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JAL-2136 merged and resolved conflicts with 80edaa84d6d9beac9f0d2c71b50b7b56fd393427

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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AppletJmol.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/StructureViewerBase.java
Merge branch 'reviews/features/JAL-2136_phyre2_integration_withJims' into merge/JAL-2136_phyre2_integration

JAL-2136 update merged code for JAL-2040 for new FileFormat/Protocol interface (JAL-2344)

Merge branch 'reviews/features/JAL-2136_phyre2_integration_withJims' into merge/JAL-2136_phyre2_integration

Merge branch 'features/JAL-2040_JAL-2137_phyre2' into reviews/features/JAL-2136_phyre2_integration_withJims

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    /src/jalview/io/AnnotationFile.java
JAL-2375 JAL-2376 First commit of implementation for Phyre2 result browsing, template parsing and structure mapping. Added fix for failing tests in SiftsClientTest, added improvement to un-offer cached option when cached data is unavailable, added improvement to include horizontal separator between structure filter options and manual input options, and other minor refactoring

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    /examples/testdata/phyre2results/56da5616b4559c93/PBS_jobid
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Merge branch 'spike/JAL-2040_JAL-2137_phyre2' into features/JAL-2040_JAL-2137_phyre2

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    /src/jalview/io/AnnotationFile.java
JAL-2356 enhanced unit test to verify reuse (or not) of file from cache

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    /src/jalview/ws/sifts/SiftsClient.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
Merge branch 'patch/JAL-2197_jpredforjnets' into develop merge was missed for 2.10.1 release!

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    /resources/lang/Messages_es.properties
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    /src/jalview/appletgui/AlignFrame.java
JAL-2105 updated for reviewed REST version 4.8

JAL-1895 suppress RNA interaction colour option

JAL-2359 add Window menu entry only after all danger of error is passed

JAL-2356 use cached Sifts file if not expired

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2354 handle error response when fetching features

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    /src/jalview/ext/ensembl/EnsemblFeatures.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
JAL-2344 handle null format, simplify JalviewFileChooser constructor

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    /src/jalview/gui/UserDefinedColours.java
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    /src/jalview/gui/WsParamSetManager.java
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    /src/jalview/io/JalviewFileChooser.java
Merge branch 'features/JAL-2320_closeChimeraAction' into develop also tidied up javadoc

JAL-2344 use ".cif" for saved mmCIF file (and refactor fetch as file)

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    /src/jalview/datamodel/PDBEntry.java
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    /src/jalview/ws/dbsources/EmblXmlSource.java
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    /src/jalview/ws/dbsources/Uniprot.java
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    /src/jalview/ws/ebi/EBIFetchClient.java
JAL-2329 tests to confirm behaviour of Java extended for loops

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    /test/jalview/datamodel/ConcurrentModificationTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-2344 corrected conversion of Type enum to FileFormat

Merge branch 'documentation/JAL-2325_release2101' into develop

JAL-2325 update release date in whatsNew

JAL-2344 FileFormat.isStructureFile replaces StructureFile.isStructureFile

Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

Merge branch 'documentation/JAL-2325_release2101' into develop

Merge branch 'develop' into trialMerge

Conflicts:

src/jalview/gui/CutAndPasteTransfer.java

test/MCview/PDBfileTest.java

test/jalview/analysis/AlignmentAnnotationUtilsTest.java

test/jalview/analysis/DnaTest.java

test/jalview/analysis/FinderTest.java

test/jalview/analysis/scoremodels/FeatureScoreModelTest.java

test/jalview/controller/AlignViewControllerTest.java

test/jalview/datamodel/AlignmentTest.java

test/jalview/ext/ensembl/EnsemblSeqProxyTest.java

test/jalview/ext/jmol/JmolParserTest.java

test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java

test/jalview/ext/paradise/TestAnnotate3D.java

test/jalview/io/gff/ExonerateHelperTest.java

test/jalview/io/gff/GffTests.java

test/jalview/structure/Mapping.java

test/jalview/structure/StructureSelectionManagerTest.java

test/jalview/structures/models/AAStructureBindingModelTest.java

test/jalview/util/MappingUtilsTest.java

test/jalview/ws/sifts/SiftsClientTest.java

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    /src/jalview/gui/AlignExportSettings.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AssociatePdbFileWithSeq.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/CutAndPasteTransfer.java
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    /src/jalview/gui/Preferences.java
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    /src/jalview/gui/StructureChooser.java
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