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

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
  1. … 487 more files in changeset.
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
  1. … 52 more files in changeset.
JAL-2325 JAL-1878 update minimum versions of JRE for running/installing on windows and OSX

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    /utils/InstallAnywhere/Jalview.iap_xml
Merge branch 'features/JAL-2326_JOptionPane-refactoring' into develop

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    /test/jalview/analysis/FinderTest.java
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    /test/jalview/util/PlatformTest.java
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    /test/jalview/util/SparseCountTest.java
JAL-2344 added FileFormatI.isStructureFile()

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    /src/jalview/io/AppletFormatAdapter.java
JAL-2345 cache generated ImageIcon per file path

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    /src/jalview/io/JalviewFileView.java
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    /test/jalview/io/JalviewFileViewTest.java
Merge branch 'documentation/JAL-2325_release2101' into develop

JAL-2325 finalise release notes

JAL-2344 dynamically determine recognised extensions for file browser

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    /src/jalview/io/JalviewFileChooser.java
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    /src/jalview/io/JalviewFileView.java