- * Returns the index (zero-based position) of a sequence in an alignment, or
- * -1 if not found.
- *
- * @param al
- * @param seq
- * @return
- */
- public static int getSequenceIndex(AlignmentI al, SequenceI seq)
- {
- int result = -1;
- int pos = 0;
- for (SequenceI alSeq : al.getSequences())
- {
- if (alSeq == seq)
- {
- result = pos;
- break;
- }
- pos++;
- }
- return result;
- }
-
- /**