- jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
- vamsasSeq[i].getSequence());
- jseqs[i].setDescription( vamsasSeq[i].getDescription() );
+ String seqId = JSEQ[i].getId() + "";
+
+ if (seqRefIds.get(seqId) != null)
+ {
+ tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ multipleView = true;
+ }
+ else
+ {
+ jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
+ vamsasSeq[i].getSequence());
+ jseq.setDescription(vamsasSeq[i].getDescription());
+ jseq.setStart(JSEQ[i].getStart());
+ jseq.setEnd(JSEQ[i].getEnd());
+ jseq.setColor(new java.awt.Color(JSEQ[i].getColour()));
+ seqRefIds.put(vamsasSeq[i].getId(), jseq);
+ tmpseqs.add( jseq );
+ }
+
+
+ if (JSEQ[i].getHidden())
+ {
+ if (hiddenSeqs == null)
+ hiddenSeqs = new Vector();
+
+
+ hiddenSeqs.addElement(
+ (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ }