+ /**
+ * create/return unique hash string for sq
+ * @param sq
+ * @return new or existing unique string for sq
+ */
+ String seqHash(SequenceI sq)
+ {
+ if (seqsToIds==null)
+ {
+ initSeqRefs();
+ }
+ if (seqsToIds.containsKey(sq))
+ {
+ return (String) seqsToIds.get(sq);
+ } else {
+ // create sequential key
+ String key = "sq"+(seqsToIds.size()+1);
+ seqsToIds.put(sq, key);
+ return key;
+ }
+ }
+ void clearSeqRefs()
+ {
+ seqRefIds.clear();
+ seqsToIds.clear();
+ }
+ void initSeqRefs()
+ {
+ if (seqsToIds==null)
+ {
+ seqsToIds = new IdentityHashMap();
+ }
+ if (seqRefIds==null)
+ {
+ seqRefIds = new Hashtable();
+ }
+ }
+ java.util.IdentityHashMap seqsToIds = null; // SequenceI->key resolution
+ java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
+
+ Vector frefedSequence = null;
+ boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+ public Jalview2XML()
+ {
+ }
+ public Jalview2XML(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ }
+
+ public void resolveFrefedSequences()
+ {
+ if (frefedSequence.size() > 0)
+ {
+ int r = 0, rSize = frefedSequence.size();
+ while (r < rSize)
+ {
+ Object[] ref = (Object[]) frefedSequence.elementAt(r);
+ if (ref != null)
+ {
+ String sref = (String) ref[0];
+ if (seqRefIds.containsKey(sref))
+ {
+ if (ref[1] instanceof jalview.datamodel.Mapping)
+ {
+ SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
+ }
+ else
+ {
+ if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
+ {
+ SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ if (ref[2] != null
+ && ref[2] instanceof jalview.datamodel.Mapping)
+ {
+ jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
+ ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
+ seq, mp.getTo(), mp.getMap());
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
+ + ref[2].getClass() + " type objects.");
+ }
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
+ + ref[1].getClass() + " type objects.");
+ }
+ frefedSequence.remove(r);
+ rSize--;
+ }
+ }
+ else
+ {
+ System.err.println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "+ref[0]+" with objecttype "+ref[1].getClass());
+ r++;
+ }
+ }
+ else
+ {
+ frefedSequence.remove(r);
+ rSize--;
+ }
+ }
+ }
+ }