+ /**
+ * Makes an alignment containing the given sequences; the sequences are
+ * added to the given alignment dataset, and the dataset is set on (shared
+ * by) the new alignment
+ *
+ * @param dataset
+ * @param seqs
+ * @return
+ */
+ protected Alignment makeCrossReferencesAlignment(Alignment dataset,
+ Alignment seqs)
+ {
+ SequenceI[] sprods = new SequenceI[seqs.getHeight()];
+ for (int s = 0; s < sprods.length; s++)
+ {
+ sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
+ if (dataset.getSequences() == null
+ || !dataset.getSequences().contains(
+ sprods[s].getDatasetSequence()))
+ {
+ dataset.addSequence(sprods[s].getDatasetSequence());
+ }
+ sprods[s].updatePDBIds();
+ }
+ Alignment al = new Alignment(sprods);
+ al.setDataset(dataset);
+ return al;
+ }
+