+ return contextAl != null && validJvresults
+ && context.getAl().get(0).isModified();
+ }
+
+ /**
+ *
+ * @return true if the ID/metadata for the input sequences were saved and
+ * sequence IDs renamed.
+ */
+ public boolean isInputUniquified()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /**
+ * Return map between ordering of alignment submitted as input, and ordering
+ * of alignment as provided by user
+ *
+ * @return int[sequence index in submitted data]==sequence index in input.
+ */
+ public int[] getOrderMap()
+ {
+ SequenceI[] contseq = contextAl.getSequencesArray();
+ int map[] = new int[contseq.length];
+ for (int i = 0; i < contseq.length; i++)
+ {
+ // TODO: optimise for large N - build a lookup hash for IDs returning
+ // order, and then lookup each sequ's original order
+ map[i] = inputOrder.getOrder().indexOf(contseq[i]);
+ }
+ return map;