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JAL-1957 JAL-1479 Further optimisation of SIFTs Client and addition of support for multi-chain mapping of uniprot <-> pdb residues

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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ws/sifts/SiftsClient.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL 1960 added code to restrict structure chooser to discover only PDB and Uniprot entries when the references are avaiable

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    /src/jalview/gui/StructureChooser.java
JAL-1479 SiftClient house keeping

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    /src/jalview/ws/sifts/SiftsClient.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/SequenceI.setDBRef to SequenceI.getDBRefs/SequenceI.setDBRefs

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    /src/jalview/datamodel/SequenceGroup.java
JAL-1955 Uniprot sequence fetcher refactor

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    /src/jalview/ws/dbsources/Uniprot.java
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    /test/jalview/ws/dbsources/UniprotTest.java
JAL-1926 JAL-1479 updated PDBfile fetcher to add sourceDBRef on importing sequences

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-1479 added support for SIFTs mapping output viewing and implemented exception handling

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    /src/jalview/api/SiftsClientI.java
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    /src/jalview/datamodel/DBRefEntry.java
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    /src/jalview/ws/sifts/MappingOutputPojo.java
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    /src/jalview/ws/sifts/SiftsClient.java
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    /src/jalview/ws/sifts/SiftsException.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-1952 bugfix

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    /src/jalview/analysis/AlignSeq.java
JAL-1887 JAL-1479 bugfix for incorrect start/end for aligned sequence mapping, and a bit of StructureSelectionManager refactoring for SIFTs

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    /src/jalview/io/SiftsClient.java
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    /src/jalview/ws/sifts/SiftsClient.java
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    /test/jalview/io/SiftsClientTest.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-1479 added basic support for SIFTs mapping - more work to follow

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    /src/jalview/analysis/AlignSeq.java
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    /src/jalview/api/SiftsClientI.java
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    /src/jalview/io/SiftsClient.java
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    /test/jalview/io/1a70.xml.gz
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    /test/jalview/io/SiftsClientTest.java
JAL-1479 implemented preferences for SIFTs / Needleman & Wunsch selection in structures preference tab

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    /src/jalview/jbgui/GPreferences.java
JAL-1942 JAL-1479 DBRefFetcher refactor

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    /src/jalview/ws/DBRefFetcher.java
JAL-1479 refactored SequenceI interface - changed getDBRef() to getDBRefs() since it returns an array of DBRefEntry

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/datamodel/DBRefEntry.java
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    /src/jalview/datamodel/SequenceGroup.java
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    /src/jalview/gui/StructureChooser.java
  1. … 13 more files in changeset.
JAL-1926 created interface for DBRefEntry

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    /src/jalview/api/DBRefEntryI.java
JAL-1926 added supporting model changes to enable saving sourceDBRef data for sequences

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    /src/jalview/datamodel/DBRefEntry.java
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    /src/jalview/datamodel/Sequence.java
JAL-1479 added SIFTS XSD and generated JAXB bindings from it

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    /schemas/sifts/alignment.xsd
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    /schemas/sifts/dataTypes.xsd
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    /schemas/sifts/eFamily.xsd
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    /src/jalview/xml/binding/sifts/Alignment.java
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    /src/jalview/xml/binding/sifts/EntityType.java
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    /src/jalview/xml/binding/sifts/Entry.java
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    /src/jalview/xml/binding/sifts/ObjectFactory.java
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    /src/jalview/xml/binding/sifts/package-info.java
JAL-1684 updated fragment alignment for example and added aligned protein and cDNA

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    /examples/estrogenReceptorCdna_aln.fa
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    /examples/estrogenReceptorCdna_frag.fa
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    /examples/estrogenReceptorProtein_aln.fa
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    /examples/estrogenReceptorProtein_frag.fa
Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

JAL-1894 add licensing

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    /test/jalview/bin/JalviewLiteTest.java
JAL-1912 JAL-1896 release notes updated

JAL-1894 update what's new

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

JAL-1912 JAL-1896 release notes updated

JAL-1544 typo fix

JAL-1894 formatting

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    /test/jalview/bin/JalviewLiteTest.java
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    /test/jalview/io/FeaturesFileTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-1894 organise imports

merge

JAL-1894 source formatting

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-1894 organise imports

JAL-1894 update release date