{\r
int i = 0;\r
SequenceI[] preds = prediction.getSeqsAsArray();\r
+ // in the future we could search for the query\r
+ // sequence in the alignment before calling this function.\r
SequenceI seqRef = al.getSequenceAt(FirstSeq);\r
int width = preds[0].getSequence().length();\r
int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r