+ /**
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
+ */
+ public int getIndex()
+ {
+ return index;
+ }
+
+ /**
+ * Defines the position of this sequence in the MSA. Use the value {@code -1}
+ * if this information is undefined.
+ *
+ * @param The
+ * position for this sequence. This value is zero-based (zero for
+ * this first sequence)
+ */
+ public void setIndex(int value)
+ {
+ index = value;
+ }
+
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ public RNA getRNA()
+ {
+ return rna;
+ }
+
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label)
+ {
+ List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ if (this.annotation != null)
+ {
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (ann.calcId != null && ann.calcId.equals(calcId)
+ && ann.label != null && ann.label.equals(label))
+ {
+ result.add(ann);
+ }
+ }
+ }
+ return result;
+ }
+
+ public String toString()
+ {
+ return getDisplayId(false);
+ }
+
+ @Override
+ public PDBEntry getPDBEntry(String pdbIdStr)
+ {
+ if (getDatasetSequence() == null
+ || getDatasetSequence().getAllPDBEntries() == null)
+ {
+ return null;
+ }
+ List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+ for (PDBEntry entry : entries)
+ {
+ if (entry.getId().equalsIgnoreCase(pdbIdStr))
+ {
+ return entry;
+ }
+ }
+ return null;
+ }
+