+ @Override
+ public SequenceI getSequenceAtAbsoluteIndex(int i)
+ {
+ SequenceI seq = null;
+ if (getHiddenSequences().getSize() > 0)
+ {
+ seq = getHiddenSequences().getHiddenSequence(i);
+ if (seq == null)
+ {
+ // didn't find the sequence in the hidden sequences, get it from the
+ // alignment
+ int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i);
+ seq = getSequenceAt(index);
+ }
+ }
+ else
+ {
+ seq = getSequenceAt(i);
+ }
+ return seq;
+ }
+