+ Vector subset = new Vector();
+ Enumeration e = annotation.elements();
+ while (e.hasMoreElements())
+ {
+ AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
+ if (ann.label != null && ann.label.equals(label))
+ {
+ subset.addElement(ann);
+ }
+ }
+ if (subset.size() == 0)
+ {
+ return null;
+ }
+ AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
+ int i = 0;
+ e = subset.elements();
+ while (e.hasMoreElements())
+ {
+ anns[i++] = (AlignmentAnnotation) e.nextElement();
+ }
+ subset.removeAllElements();
+ return anns;
+ }
+
+ @Override
+ public boolean updatePDBIds()
+ {
+ if (datasetSequence != null)
+ {
+ // TODO: could merge DBRefs
+ return datasetSequence.updatePDBIds();
+ }
+ if (dbrefs == null || dbrefs.length == 0)
+ {
+ return false;
+ }
+ boolean added = false;
+ for (DBRefEntry dbr : dbrefs)
+ {
+ if (DBRefSource.PDB.equals(dbr.getSource()))
+ {
+ /*
+ * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the
+ * PDB id is not already present in a 'matching' PDBEntry
+ * Constructor parses out a chain code if appended to the accession id
+ * (a fudge used to 'store' the chain code in the DBRef)
+ */
+ PDBEntry pdbe = new PDBEntry(dbr);
+ added |= addPDBId(pdbe);
+ }
+ }
+ return added;
+ }
+
+ @Override
+ public void transferAnnotation(SequenceI entry, Mapping mp)
+ {
+ if (datasetSequence != null)
+ {
+ datasetSequence.transferAnnotation(entry, mp);
+ return;
+ }
+ if (entry.getDatasetSequence() != null)
+ {
+ transferAnnotation(entry.getDatasetSequence(), mp);
+ return;
+ }
+ // transfer any new features from entry onto sequence
+ if (entry.getSequenceFeatures() != null)
+ {
+
+ SequenceFeature[] sfs = entry.getSequenceFeatures();
+ for (int si = 0; si < sfs.length; si++)
+ {
+ SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
+ : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
+ if (sf != null && sf.length > 0)
+ {
+ for (int sfi = 0; sfi < sf.length; sfi++)
+ {
+ addSequenceFeature(sf[sfi]);
+ }
+ }
+ }
+ }
+
+ // transfer PDB entries
+ if (entry.getAllPDBEntries() != null)
+ {
+ Enumeration e = entry.getAllPDBEntries().elements();
+ while (e.hasMoreElements())
+ {
+ PDBEntry pdb = (PDBEntry) e.nextElement();
+ addPDBId(pdb);
+ }
+ }
+ // transfer database references
+ DBRefEntry[] entryRefs = entry.getDBRefs();
+ if (entryRefs != null)
+ {
+ for (int r = 0; r < entryRefs.length; r++)
+ {
+ DBRefEntry newref = new DBRefEntry(entryRefs[r]);
+ if (newref.getMap() != null && mp != null)
+ {
+ // remap ref using our local mapping
+ }
+ // we also assume all version string setting is done by dbSourceProxy
+ /*
+ * if (!newref.getSource().equalsIgnoreCase(dbSource)) {
+ * newref.setSource(dbSource); }
+ */
+ addDBRef(newref);
+ }
+ }
+ }
+
+ /**
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
+ */
+ @Override
+ public int getIndex()
+ {
+ return index;
+ }
+
+ /**
+ * Defines the position of this sequence in the MSA. Use the value {@code -1}
+ * if this information is undefined.
+ *
+ * @param The
+ * position for this sequence. This value is zero-based (zero for
+ * this first sequence)
+ */
+ @Override
+ public void setIndex(int value)
+ {
+ index = value;
+ }
+
+ @Override
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ @Override
+ public RNA getRNA()
+ {
+ return rna;
+ }
+
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label)
+ {
+ List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ if (this.annotation != null)
+ {
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (ann.calcId != null && ann.calcId.equals(calcId)
+ && ann.label != null && ann.label.equals(label))
+ {
+ result.add(ann);
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String toString()
+ {
+ return getDisplayId(false);
+ }
+
+ @Override
+ public PDBEntry getPDBEntry(String pdbIdStr)
+ {
+ if (getDatasetSequence() != null)
+ {
+ return getDatasetSequence().getPDBEntry(pdbIdStr);
+ }
+ if (pdbIds == null)
+ {
+ return null;
+ }
+ List<PDBEntry> entries = getAllPDBEntries();
+ for (PDBEntry entry : entries)
+ {
+ if (entry.getId().equalsIgnoreCase(pdbIdStr))
+ {
+ return entry;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public List<DBRefEntry> getPrimaryDBRefs()
+ {
+ if (datasetSequence != null)
+ {
+ return datasetSequence.getPrimaryDBRefs();
+ }
+ if (dbrefs == null || dbrefs.length == 0)
+ {
+ return Collections.emptyList();
+ }
+ synchronized (dbrefs)
+ {
+ List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+ DBRefEntry[] tmp = new DBRefEntry[1];
+ for (DBRefEntry ref : dbrefs)
+ {
+ if (!ref.isPrimaryCandidate())
+ {
+ continue;
+ }
+ if (ref.hasMap())
+ {
+ MapList mp = ref.getMap().getMap();
+ if (mp.getFromLowest() > start || mp.getFromHighest() < end)
+ {
+ // map only involves a subsequence, so cannot be primary
+ continue;
+ }
+ }
+ // whilst it looks like it is a primary ref, we also sanity check type
+ if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
+ DBRefUtils.getCanonicalName(ref.getSource())))
+ {
+ // PDB dbrefs imply there should be a PDBEntry associated
+ // TODO: tighten PDB dbrefs
+ // formally imply Jalview has actually downloaded and
+ // parsed the pdb file. That means there should be a cached file
+ // handle on the PDBEntry, and a real mapping between sequence and
+ // extracted sequence from PDB file
+ PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
+ if (pdbentry != null && pdbentry.getFile() != null)
+ {
+ primaries.add(ref);
+ }
+ continue;
+ }
+ // check standard protein or dna sources
+ tmp[0] = ref;
+ DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+ if (res != null && res[0] == tmp[0])
+ {
+ primaries.add(ref);
+ continue;
+ }
+ }
+ return primaries;
+ }
+ }
+
+}