+
+ /**
+ * Process a parsed chain to construct and return a Sequence, and add it to
+ * the list of sequences parsed.
+ *
+ * @param chain
+ * @return
+ */
+ protected SequenceI postProcessChain(PDBChain chain)
+ {
+ SequenceI dataset = chain.sequence;
+ dataset.setName(id + "|" + dataset.getName());
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id);
+ entry.setType(PDBEntry.Type.PDB);
+ entry.setProperty(new Hashtable());
+ if (chain.id != null)
+ {
+ // entry.getProperty().put("CHAIN", chains.elementAt(i).id);
+ entry.setChainCode(String.valueOf(chain.id));
+ }
+ if (inFile != null)
+ {
+ entry.setFile(inFile.getAbsolutePath());
+ }
+ else
+ {
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
+ }
+ dataset.addPDBId(entry);
+ // PDBChain objects maintain reference to dataset
+ SequenceI chainseq = dataset.deriveSequence();
+ seqs.addElement(chainseq);
+
+ AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+
+ if (chainannot != null && visibleChainAnnotation)
+ {
+ for (int ai = 0; ai < chainannot.length; ai++)
+ {
+ chainannot[ai].visible = visibleChainAnnotation;
+ annotations.addElement(chainannot[ai]);
+ }
+ }
+ return chainseq;
+ }
+
+ public static boolean isCalcIdHandled(String calcId)
+ {
+ return calcId != null && (CALC_ID_PREFIX.equals(calcId));
+ }
+
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+ String pdbFile)
+ {
+ return alan.getCalcId() != null
+ && CALC_ID_PREFIX.equals(alan.getCalcId())
+ && pdbFile.equals(alan.getProperty("PDBID"));
+ }
+
+ public static String relocateCalcId(String calcId,
+ Hashtable<String, String> alreadyLoadedPDB) throws Exception
+ {
+ int s = CALC_ID_PREFIX.length(), end = calcId
+ .indexOf(CALC_ID_PREFIX, s);
+ String between = calcId.substring(s, end - 1);
+ return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
+ + calcId.substring(end);
+ }
+