--- /dev/null
+package jalview.analysis;
+
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.ws.SequenceFetcherFactory;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+public class CrossRefs
+{
+ /**
+ * Finds cross-references for sequences from a specified source database.
+ * These may be found in four ways:
+ * <ul>
+ * <li>as a DBRefEntry on the known sequence, which has a mapped-to sequence</li>
+ * <li>a sequence of complementary type in the alignment dataset, which has a
+ * DBRefEntry to one of the known sequence's 'direct' DBRefs</li>
+ * <li>a sequence of complementary type in the alignment, which has a
+ * DBRefEntry to one of the known sequence's 'cross-ref' DBRefs</li>
+ * <li>by fetching the accession from the remote database</li>
+ * </ul>
+ *
+ * @param seqs
+ * the sequences whose cross-references we are searching for
+ * @param dna
+ * true if the sequences are from a nucleotide alignment, else false
+ * @param source
+ * the database source we want cross-references to
+ * @param dataset
+ * the alignment dataset the sequences belong to
+ * @return an alignment containing cross-reference sequences, or null if none
+ * found
+ */
+ public static AlignmentI findXrefSequences(SequenceI[] seqs, boolean dna,
+ String source, AlignmentI dataset)
+ {
+ List<SequenceI> foundSeqs = new ArrayList<SequenceI>();
+ AlignedCodonFrame mappings = new AlignedCodonFrame();
+
+ for (SequenceI seq : seqs)
+ {
+ if (dna != Comparison.isNucleotide(seq))
+ {
+ /*
+ * mixed alignment, and this sequence is of the wrong type
+ */
+ continue;
+ }
+
+ /*
+ * get this sequence's dbrefs to source database (if any)
+ */
+ List<DBRefEntry> sourceRefs = DBRefUtils.searchRefsForSource(
+ seq.getDBRefs(), source);
+
+ /*
+ * first extract any mapped sequences from sourceRefs
+ */
+ findMappedDbrefs(seq, sourceRefs, foundSeqs, mappings);
+
+ /*
+ * for remaining sourceRefs, try to match a
+ * complementary sequence in the dataset
+ */
+ findIndirectCrossReferences(seq, source, sourceRefs, dataset,
+ foundSeqs, mappings);
+
+ /*
+ * fetch any remaining sourceRefs from the source database
+ */
+ fetchCrossReferences(seq, sourceRefs, foundSeqs, mappings, dna,
+ dataset);
+ }
+
+ if (foundSeqs.isEmpty())
+ {
+ return null;
+ }
+ AlignmentI crossRefs = new Alignment(
+ foundSeqs.toArray(new SequenceI[foundSeqs.size()]));
+ crossRefs.addCodonFrame(mappings);
+ return crossRefs;
+ }
+
+ /**
+ * Looks for DBRefEntrys to 'source' which have a mapping to a sequence. If
+ * found, adds the sequence to foundSeqs and removes the dbref from the list.
+ *
+ * @param seq
+ * the dataset sequence we are searching from
+ * @param sourceRefs
+ * the sequence's dbrefs to 'source'
+ * @param foundSeqs
+ * a list of cross-references to add to
+ * @param mappings
+ * a set of sequence mappings to add to
+ * @return
+ */
+ static void findMappedDbrefs(SequenceI seq, List<DBRefEntry> sourceRefs,
+ List<SequenceI> foundSeqs, AlignedCodonFrame mappings)
+ {
+ Iterator<DBRefEntry> refs = sourceRefs.iterator();
+ while (refs.hasNext())
+ {
+ DBRefEntry dbref = refs.next();
+ Mapping map = dbref.getMap();
+ if (map != null)
+ {
+ SequenceI mappedTo = map.getTo();
+ if (mappedTo != null)
+ {
+ foundSeqs.add(new Sequence(mappedTo));
+ refs.remove();
+
+ /*
+ * check mapping is not 'direct' (it shouldn't be if we reach here)
+ * and add mapping (dna-to-peptide or vice versa) to the set
+ */
+ MapList mapList = map.getMap();
+ int fromRatio = mapList.getFromRatio();
+ int toRatio = mapList.getToRatio();
+ if (fromRatio != toRatio)
+ {
+ if (fromRatio == 3)
+ {
+ mappings.addMap(seq, mappedTo, mapList);
+ }
+ else
+ {
+ mappings.addMap(mappedTo, seq, mapList.getInverse());
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Tries to fetch seq's database references to 'source' database, and add them
+ * to the foundSeqs list. If found, tries to make a mapping between seq and
+ * the retrieved sequence and insert it into the database reference.
+ *
+ * @param seq
+ * @param sourceRefs
+ * @param foundSeqs
+ * @param mappings
+ * @param dna
+ */
+ static void fetchCrossReferences(SequenceI seq,
+ List<DBRefEntry> sourceRefs, List<SequenceI> foundSeqs,
+ AlignedCodonFrame mappings, boolean dna, AlignmentI dataset)
+ {
+ ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
+ SequenceI[] retrieved;
+ try
+ {
+ retrieved = sftch.getSequences(sourceRefs, !dna);
+ } catch (Exception e)
+ {
+ System.err
+ .println("Problem whilst retrieving cross references for Sequence : "
+ + seq.getName());
+ e.printStackTrace();
+ return;
+ }
+
+ if (retrieved != null)
+ {
+ updateDbrefMappings(dna, seq, sourceRefs, retrieved, mappings);
+
+ SequenceIdMatcher matcher = new SequenceIdMatcher(
+ dataset.getSequences());
+ List<SequenceFeature> copiedFeatures = new ArrayList<SequenceFeature>();
+ CrossRef me = new CrossRef();
+ for (int rs = 0; rs < retrieved.length; rs++)
+ {
+ // TODO: examine each sequence for 'redundancy'
+ DBRefEntry[] dbr = retrieved[rs].getDBRefs();
+ if (dbr != null && dbr.length > 0)
+ {
+ for (int di = 0; di < dbr.length; di++)
+ {
+ // find any entry where we should put in the sequence being
+ // cross-referenced into the map
+ Mapping map = dbr[di].getMap();
+ if (map != null)
+ {
+ if (map.getTo() != null && map.getMap() != null)
+ {
+ SequenceI matched = matcher.findIdMatch(map.getTo());
+ if (matched != null)
+ {
+ /*
+ * already got an xref to this sequence; update this
+ * map to point to the same sequence, and add
+ * any new dbrefs to it
+ */
+ for (DBRefEntry ref : map.getTo().getDBRefs())
+ {
+ matched.addDBRef(ref); // add or update mapping
+ }
+ map.setTo(matched);
+ }
+ else
+ {
+ matcher.add(map.getTo());
+ }
+ try
+ {
+ // compare ms with dss and replace with dss in mapping
+ // if map is congruent
+ SequenceI ms = map.getTo();
+ int sf = map.getMap().getToLowest();
+ int st = map.getMap().getToHighest();
+ SequenceI mappedrg = ms.getSubSequence(sf, st);
+ // SequenceI loc = dss.getSubSequence(sf, st);
+ if (mappedrg.getLength() > 0
+ && ms.getSequenceAsString().equals(
+ seq.getSequenceAsString()))
+ // && mappedrg.getSequenceAsString().equals(
+ // loc.getSequenceAsString()))
+ {
+ String msg = "Mapping updated from " + ms.getName()
+ + " to retrieved crossreference "
+ + seq.getName();
+ System.out.println(msg);
+ // method to update all refs of existing To on
+ // retrieved sequence with dss and merge any props
+ // on To onto dss.
+ map.setTo(seq);
+ /*
+ * copy sequence features as well, avoiding
+ * duplication (e.g. same variation from 2
+ * transcripts)
+ */
+ SequenceFeature[] sfs = ms.getSequenceFeatures();
+ if (sfs != null)
+ {
+ for (SequenceFeature feat : sfs)
+ {
+ /*
+ * we override SequenceFeature.equals here (but
+ * not elsewhere) to ignore Parent attribute
+ * TODO not quite working yet!
+ */
+ if (!copiedFeatures
+ .contains(me.new MySequenceFeature(feat)))
+ {
+ seq.addSequenceFeature(feat);
+ copiedFeatures.add(feat);
+ }
+ }
+ }
+ }
+ mappings.addMap(retrieved[rs].getDatasetSequence(),
+ map.getTo(), map.getMap());
+ } catch (Exception e)
+ {
+ System.err
+ .println("Exception when consolidating Mapped sequence set...");
+ e.printStackTrace(System.err);
+ }
+ }
+ }
+ }
+ }
+ retrieved[rs].updatePDBIds();
+ foundSeqs.add(retrieved[rs]);
+ }
+ }
+ }
+
+ /**
+ * Searches the alignment for a sequence of complementary type to 'seq' which
+ * shares a DBRefEntry with it. If found, adds the sequence to foundSeqs and
+ * removes the resolved sourceRef from the search list.
+ *
+ * @param seq
+ * @param source
+ * @param sourceRefs
+ * @param dataset
+ * @param foundSeqs
+ * @param mappings
+ * @return
+ */
+ static void findIndirectCrossReferences(SequenceI seq, String source,
+ List<DBRefEntry> sourceRefs, AlignmentI dataset,
+ List<SequenceI> foundSeqs, AlignedCodonFrame mappings)
+ {
+ Iterator<DBRefEntry> refs = sourceRefs.iterator();
+ while (refs.hasNext())
+ {
+ DBRefEntry dbref = refs.next();
+ boolean found = searchDatasetForCrossReference(seq, dbref, dataset,
+ foundSeqs, mappings);
+ if (found)
+ {
+ refs.remove();
+ }
+ }
+ }
+
+ /**
+ * Searches the dataset for a sequence of opposite type to 'excluding', which
+ * has a cross-reference matching dbref. If found, adds the sequence to
+ * foundSeqs and removes dbref from the search list.
+ *
+ * @param excluding
+ * a sequence to ignore (start point of search)
+ * @param dbref
+ * a cross-reference to try to match
+ * @param dataset
+ * sequences to search in
+ * @param foundSeqs
+ * result list to add to
+ * @param mappings
+ * a set of sequence mappings to add to
+ * @return true if relationship found and sequence added
+ */
+ static boolean searchDatasetForCrossReference(SequenceI excluding,
+ DBRefEntry dbref, AlignmentI dataset, List<SequenceI> foundSeqs,
+ AlignedCodonFrame mappings)
+ {
+ boolean fromNucleotide = Comparison.isNucleotide(excluding);
+ boolean found = false;
+ if (dataset == null)
+ {
+ return false;
+ }
+ if (dataset.getSequences() == null)
+ {
+ return false;
+ }
+ List<SequenceI> ds;
+ synchronized (ds = dataset.getSequences())
+ {
+ for (SequenceI nxt : ds)
+ {
+ if (nxt != null)
+ {
+ if (nxt.getDatasetSequence() != null)
+ {
+ System.err
+ .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
+ }
+ if (nxt == excluding || nxt == excluding.getDatasetSequence())
+ {
+ continue;
+ }
+ if (foundSeqs.contains(nxt))
+ {
+ /*
+ * already added this sequence to cross-refs
+ */
+ continue;
+ }
+ boolean isDna = Comparison.isNucleotide(nxt);
+ if (isDna == fromNucleotide)
+ {
+ /*
+ * skip this sequence - wrong molecule type
+ */
+ continue;
+ }
+
+ /*
+ * check if this sequence has any dbref matching source and accession
+ * (version and mapping may differ)
+ */
+ List<DBRefEntry> candidates = DBRefUtils.searchRefs(
+ nxt.getDBRefs(), dbref);
+
+ if (candidates.isEmpty())
+ {
+ continue;
+ }
+ found = true;
+ foundSeqs.add(nxt);
+ if (mappings != null)
+ {
+ // don't search if we aren't given a codon map object
+ for (DBRefEntry candidate : candidates)
+ {
+ if (candidate.hasMap())
+ {
+ Mapping mapping = candidate.getMap();
+ MapList map = mapping.getMap();
+ if (mapping.getTo() != null
+ && map.getFromRatio() != map.getToRatio())
+ {
+ if (fromNucleotide)
+ {
+ // map is from dna seq to a protein product
+ mappings.addMap(excluding, nxt, map);
+ }
+ else
+ {
+ // map is from protein seq to its coding dna
+ mappings.addMap(nxt, excluding, map.getInverse());
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return found;
+ }
+
+ /**
+ * Updates any empty mappings in the cross-references with one to a compatible
+ * retrieved sequence if found, and adds any new mappings to the
+ * AlignedCodonFrame
+ *
+ * @param dna
+ * @param mapFrom
+ * @param xrefs
+ * @param retrieved
+ * @param mappings
+ */
+ static void updateDbrefMappings(boolean dna, SequenceI mapFrom,
+ List<DBRefEntry> xrefs, SequenceI[] retrieved,
+ AlignedCodonFrame mappings)
+ {
+ SequenceIdMatcher matcher = new SequenceIdMatcher(retrieved);
+ for (DBRefEntry xref : xrefs)
+ {
+ if (!xref.hasMap())
+ {
+ String targetSeqName = xref.getSource() + "|"
+ + xref.getAccessionId();
+ SequenceI[] matches = matcher.findAllIdMatches(targetSeqName);
+ if (matches == null)
+ {
+ return;
+ }
+ for (SequenceI seq : matches)
+ {
+ MapList mapping = null;
+ if (dna)
+ {
+ mapping = AlignmentUtils.mapCdnaToProtein(seq, mapFrom);
+ }
+ else
+ {
+ mapping = AlignmentUtils.mapCdnaToProtein(mapFrom, seq);
+ if (mapping != null)
+ {
+ mapping = mapping.getInverse();
+ }
+ }
+ if (mapping != null)
+ {
+ xref.setMap(new Mapping(seq, mapping));
+ if (dna)
+ {
+ AlignmentUtils.computeProteinFeatures(mapFrom, seq, mapping);
+ }
+ if (dna)
+ {
+ mappings.addMap(mapFrom, seq, mapping);
+ }
+ else
+ {
+ mappings.addMap(seq, mapFrom, mapping.getInverse());
+ }
+ continue;
+ }
+ }
+ }
+ }
+ }
+}
--- /dev/null
+package jalview.analysis;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotSame;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.MapList;
+import jalview.ws.SequenceFetcher;
+import jalview.ws.SequenceFetcherFactory;
+
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class CrossRefsTest
+{
+
+ /**
+ * Test for finding 'product' sequences for the case where the selected
+ * sequence has a dbref with a mapping to a sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testFindXrefSequences_fromDbRefMap()
+ {
+ /*
+ * two peptide sequences each with a DBRef and SequenceFeature
+ */
+ SequenceI pep1 = new Sequence("Q9ZTS2", "MALFQRSV");
+ pep1.addDBRef(new DBRefEntry("Pfam", "0", "PF00111"));
+ pep1.addSequenceFeature(new SequenceFeature("type", "desc", 12, 14, 1f,
+ "group"));
+ SequenceI pep2 = new Sequence("P30419", "MTRRSQIF");
+ pep2.addDBRef(new DBRefEntry("PDB", "0", "3JTK"));
+ pep2.addSequenceFeature(new SequenceFeature("type2", "desc2", 13, 15,
+ 12f, "group2"));
+
+ /*
+ * nucleotide sequence (to go in the alignment)
+ */
+ SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+
+ /*
+ * add DBRefEntry's to dna1 with mappings from dna to both peptides
+ */
+ MapList mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 },
+ 3, 1);
+ Mapping map = new Mapping(pep1, mapList);
+ DBRefEntry dbRef1 = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
+ dna1.addDBRef(dbRef1);
+ mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 }, 3, 1);
+ map = new Mapping(pep2, mapList);
+ DBRefEntry dbRef2 = new DBRefEntry("UNIPROT", "0", "P30419", map);
+ dna1.addDBRef(dbRef2);
+
+ /*
+ * find UNIPROT xrefs for nucleotide sequence - it should pick up
+ * mapped sequences
+ */
+ AlignmentI al = new Alignment(new SequenceI[] { dna1 });
+ AlignmentI xrefs = CrossRefs.findXrefSequences(
+ new SequenceI[] { dna1 },
+ true, "UNIPROT", al);
+ assertEquals(2, xrefs.getHeight());
+
+ /*
+ * cross-refs alignment holds copies of the mapped sequences
+ * including copies of their dbrefs and features
+ */
+ checkCopySequence(pep1, xrefs.getSequenceAt(0));
+ checkCopySequence(pep2, xrefs.getSequenceAt(1));
+ }
+
+ /**
+ * Test for finding 'product' sequences for the case where only an indirect
+ * xref is found - not on the peptide sequence but on a nucleotide sequence in
+ * the alignment which which it shares a protein dbref
+ */
+ @Test(groups = { "Functional" })
+ public void testFindXrefSequences_indirectDbrefToNucleotide()
+ {
+ /*
+ * Alignment setup:
+ * - peptide dbref UNIPROT|Q9ZTS2
+ * - nucleotide dbref EMBL|AF039662, UNIPROT|Q9ZTS2
+ */
+ SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS");
+ uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+ SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+ emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
+ emblSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+
+ /*
+ * find EMBL xrefs for peptide sequence - it has no direct
+ * dbrefs, but the 'corresponding' nucleotide sequence does, so is returned
+ */
+ /*
+ * Find EMBL xrefs for peptide
+ * - it has no EMBL dbref of its own
+ * - but nucleotide with matching peptide dbref does, so is returned
+ */
+ AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
+ AlignmentI xrefs = CrossRefs.findXrefSequences(
+ new SequenceI[] { uniprotSeq }, false, "EMBL", al);
+ assertEquals(1, xrefs.getHeight());
+ assertSame(emblSeq, xrefs.getSequenceAt(0));
+ }
+
+ /**
+ * Test for finding 'product' sequences for the case where only an indirect
+ * xref is found - not on the nucleotide sequence but on a peptide sequence in
+ * the alignment which which it shares a nucleotide dbref
+ */
+ @Test(groups = { "Functional" })
+ public void testFindXrefSequences_indirectDbrefToProtein()
+ {
+ /*
+ * Alignment setup:
+ * - nucleotide dbref EMBL|AF039662
+ * - peptide dbrefs EMBL|AF039662, UNIPROT|Q9ZTS2
+ */
+ SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+ emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
+ SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS");
+ uniprotSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
+ uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+
+ /*
+ * Find UNIPROT xrefs for nucleotide
+ * - it has no UNIPROT dbref of its own
+ * - but peptide with matching nucleotide dbref does, so is returned
+ */
+ AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
+ AlignmentI xrefs = CrossRefs.findXrefSequences(
+ new SequenceI[] { emblSeq }, true, "UNIPROT", al);
+ assertEquals(1, xrefs.getHeight());
+ assertSame(uniprotSeq, xrefs.getSequenceAt(0));
+ }
+
+ /**
+ * Test for finding 'product' sequences for the case where the selected
+ * sequence has no dbref to the desired source, and there are no indirect
+ * references via another sequence in the alignment
+ */
+ @Test(groups = { "Functional" })
+ public void testFindXrefSequences_noDbrefs()
+ {
+ /*
+ * two nucleotide sequences, one with UNIPROT dbref
+ */
+ SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+ SequenceI dna2 = new Sequence("AJ307031", "AAACCCTTT");
+
+ /*
+ * find UNIPROT xrefs for peptide sequence - it has no direct
+ * dbrefs, and the other sequence (which has a UNIPROT dbref) is not
+ * equatable to it, so no results found
+ */
+ AlignmentI al = new Alignment(new SequenceI[] { dna1, dna2 });
+ AlignmentI xrefs = CrossRefs.findXrefSequences(
+ new SequenceI[] { dna2 },
+ true, "UNIPROT", al);
+ assertNull(xrefs);
+ }
+
+ /**
+ * Test for finding 'product' sequences for the case where the selected
+ * sequence has a dbref with no mapping, triggering a fetch from database
+ */
+ @Test(groups = { "Functional" })
+ public void testFindXrefSequences_withFetch()
+ {
+ SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P30419"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
+ final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
+ final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
+
+ SequenceFetcher mockFetcher = new SequenceFetcher()
+ {
+
+ @Override
+ public boolean isFetchable(String source)
+ {
+ return true;
+ }
+
+ @Override
+ public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
+ {
+ return new SequenceI[] { pep1, pep2 };
+ }
+ };
+ SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+
+ /*
+ * find UNIPROT xrefs for nucleotide sequence
+ */
+ AlignmentI al = new Alignment(new SequenceI[] { dna1 });
+ AlignmentI xrefs = CrossRefs.findXrefSequences(
+ new SequenceI[] { dna1 },
+ true, "UNIPROT", al);
+ assertEquals(2, xrefs.getHeight());
+ assertSame(pep1, xrefs.getSequenceAt(0));
+ assertSame(pep2, xrefs.getSequenceAt(1));
+ }
+
+ /**
+ * Helper method to assert seq1 looks like a copy of seq2
+ *
+ * @param seq1
+ * @param seq2
+ */
+ private void checkCopySequence(SequenceI seq1, SequenceI seq2)
+ {
+ assertNotSame(seq1, seq2);
+ assertEquals(seq1.getName(), seq2.getName());
+ assertEquals(seq1.getStart(), seq2.getStart());
+ assertEquals(seq1.getEnd(), seq2.getEnd());
+ assertEquals(seq1.getSequenceAsString(), seq2.getSequenceAsString());
+
+ /*
+ * compare dbrefs
+ */
+ assertArrayEquals(seq1.getDBRefs(), seq2.getDBRefs());
+ // check one to verify a copy, not the same object
+ if (seq1.getDBRefs().length > 0)
+ {
+ assertNotSame(seq1.getDBRefs()[0], seq2.getDBRefs()[0]);
+ }
+
+ /*
+ * compare features
+ */
+ assertArrayEquals(seq1.getSequenceFeatures(),
+ seq2.getSequenceFeatures());
+ if (seq1.getSequenceFeatures().length > 0)
+ {
+ assertNotSame(seq1.getSequenceFeatures()[0],
+ seq2.getSequenceFeatures()[0]);
+ }
+ }
+
+ /**
+ * Test for finding 'product' sequences for the case where the selected
+ * sequence has two dbrefs with no mapping, triggering a fetch from database.
+ *
+ * @see http://issues.jalview.org/browse/JAL-2029
+ */
+ @Test(groups = { "Functional" })
+ public void testFindXrefSequences_withFetchMultipleRefs()
+ {
+ /*
+ * EMBL|X07547 has a
+ */
+ SequenceI dna1 = new Sequence("X07547", "GGGGCAGCACAAGAAC");
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "B0BCM4"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P0CE20"));
+ final SequenceI pep1 = new Sequence("B0BCM4", "MGKGIL");
+ final SequenceI pep2 = new Sequence("P0CE20", "MGKGIL");
+
+ SequenceFetcher mockFetcher = new SequenceFetcher()
+ {
+ int call = 0;
+
+ @Override
+ public boolean isFetchable(String source)
+ {
+ return true;
+ }
+ @Override
+ public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
+ {
+ // pending Mockito with its thenReturn(pep1).thenReturn(pep2) syntax!
+ return new SequenceI[] { call++ == 0 ? pep1 : pep2 };
+ }
+ };
+ SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+
+ /*
+ * find UNIPROT xrefs for nucleotide sequence
+ */
+ AlignmentI al = new Alignment(new SequenceI[] { dna1 });
+ AlignmentI xrefs = CrossRefs.findXrefSequences(
+ new SequenceI[] { dna1 },
+ true, "UNIPROT", al);
+ assertEquals(2, xrefs.getHeight());
+ assertSame(pep1, xrefs.getSequenceAt(0));
+ assertSame(pep2, xrefs.getSequenceAt(1));
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff