+ @Override
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ @Override
+ public RNA getRNA()
+ {
+ return rna;
+ }
+
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label)
+ {
+ return getAlignmentAnnotations(calcId, label, null, true);
+ }
+
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description)
+ {
+ return getAlignmentAnnotations(calcId, label, description, false);
+ }
+
+ private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description, boolean ignoreDescription)
+ {
+ List<AlignmentAnnotation> result = new ArrayList<>();
+ if (this.annotation != null)
+ {
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if ((ann.calcId != null && ann.calcId.equals(calcId))
+ && (ann.label != null && ann.label.equals(label))
+ && ((ignoreDescription && description == null)
+ || (ann.description != null
+ && ann.description.equals(description))))
+
+ {
+ 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;
+ }
+
+ private List<DBRefEntry> tmpList;
+
+ @Override
+ public List<DBRefEntry> getPrimaryDBRefs()
+ {
+ if (datasetSequence != null)
+ {
+ return datasetSequence.getPrimaryDBRefs();
+ }
+ if (dbrefs == null || dbrefs.size() == 0)
+ {
+ return Collections.emptyList();
+ }
+ synchronized (dbrefs)
+ {
+ if (refModCount == dbrefs.getModCount() && primaryRefs != null)
+ {
+ return primaryRefs; // no changes
+ }
+ refModCount = dbrefs.getModCount();
+ List<DBRefEntry> primaries = (primaryRefs == null
+ ? (primaryRefs = new ArrayList<>())
+ : primaryRefs);
+ primaries.clear();
+ if (tmpList == null)
+ {
+ tmpList = new ArrayList<>();
+ tmpList.add(null); // for replacement
+ }
+ for (int i = 0, n = dbrefs.size(); i < n; i++)
+ {
+ DBRefEntry ref = dbrefs.get(i);
+ 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 (DBRefSource.PDB_CANONICAL_NAME
+ .equals(ref.getCanonicalSourceName()))
+ {
+ // 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)
+ {
+ continue;
+ }
+ }
+ else
+ {
+ // check standard protein or dna sources
+ tmpList.set(0, ref);
+ List<DBRefEntry> res = DBRefUtils.selectDbRefs(!isProtein(),
+ tmpList);
+ if (res == null || res.get(0) != tmpList.get(0))
+ {
+ continue;
+ }
+ }
+ primaries.add(ref);
+ }
+
+ // version must be not null, as otherwise it will not be a candidate,
+ // above
+ DBRefUtils.ensurePrimaries(this, primaries);
+ return primaries;
+ }
+ }
+