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JAL-2106 fix (last one!) remove the Sequence.sourceDBRef field!

JAL-2154 ENSEMBL and Uniprot tests

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    /test/jalview/io/CrossRef2xmlTests.java
JAL-2154 report any db fetch failures as a fail at end

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    /test/jalview/io/CrossRef2xmlTests.java
JAL-2154 ensure pass increments actually result in a termination

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    /test/jalview/io/CrossRef2xmlTests.java
JAL-2154 catch and report a failures when xrefed project didn’t seem to have associated file (possibly due to failed ref retrieval)

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    /test/jalview/io/CrossRef2xmlTests.java
JAL-2154 check that xref is a coding xref before adding sequence to retrieved xrefs

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    /src/jalview/analysis/CrossRef.java
JAL-2154 don’t add any remaining xrefed sequences of the wrong molecule type to the alignment

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    /src/jalview/analysis/AlignmentUtils.java
JAL-2154 drop PDB from Protein db list to remove from fetch cross-refs menu

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    /src/jalview/datamodel/DBRefSource.java
JAL-2154 Defer failing cross-ref combinations that didn’t result in a new alignment window till end of test

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    /test/jalview/io/CrossRef2xmlTests.java
JAL-2154 check that CDS panel is only nucleotide, and protein panel is only Protein for retrieved cross-refs

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    /test/jalview/io/CrossRef2xmlTests.java
JAL-2106 JAL-2154 fix test for additional reference transferred from locus to CDS as well as Peptide

JAL-2106 JAL-2154 cross-refs from Ensembl should verify as cross refs only

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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/ext/ensembl/EnsemblSymbol.java
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    /src/jalview/ext/ensembl/EnsemblXref.java
JAL-2106 tighten DBRefEntry primary seq test for PDB

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    /test/jalview/datamodel/SequenceTest.java
JAL-2154 JAL-2106 transfer primary refs to CDS for makeCDS

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    /src/jalview/analysis/AlignmentUtils.java
JAL-2154 copy and paste error

Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation

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    /src/jalview/analysis/AlignmentUtils.java
Merge branch 'refactor/JAL-2106_sourceDbRef_revision' into trailm

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    /src/jalview/datamodel/Sequence.java
Merge branch 'develop' into bug/JAL-2154projectMappings

Conflicts:

src/jalview/gui/AlignFrame.java - propagated MessageManager tweak to jalview/gui/CrossRefAction.java

Merge branch 'develop' into refactor/JAL-2106_sourceDbRef_revision

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    /src/jalview/analysis/AlignmentUtils.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-2178 remove duplicate Uniprot db source

JAL-1424 duplicate key removed

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    /resources/lang/Messages_es.properties
JAL-2106 FIXME for test failure

JAL-2106 TODO - verify Embl primary refs get added

JAL-2106 tidy up and comments for DBRefFetcher

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    /src/jalview/ws/DBRefFetcher.java
JAL-2106 javadoc for sifts mapping method

JAL-2106 prevent SIFTS mappings for sequences that don’t look like protein

JAL-2106 removed setSourceDBRef, refactor getSourceDBRef to getPrimaryDBRefs * minimal test for PDB cornercase * minimal revision of AlignmentUtils/Tests, CrossRef * basic patch to SIFTSClient - need to revisit

TODO

* jalview.io.StructureFile re ‘PDB’ primary dbrefs generated from filenames.

* verify primary refs added correctly for Uniprot, EMBL, Ensembl and EnsemblGenomes in their unit tests.

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/ws/dbsources/Uniprot.java
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    /src/jalview/ws/sifts/SiftsClient.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-2106 stricter check for 1:1 mapping (same numbering on both sides, and word size == 1)

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    /src/jalview/datamodel/DBRefEntry.java
JAL-2106 rejig test to minimally verify patch that getPDBEntry can be called on local and dataset sequence

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    /test/jalview/datamodel/SequenceTest.java
JAL-2106 convenience method to find all dbsource names via reflection

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    /src/jalview/datamodel/DBRefSource.java