+
+ /**
+ * 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;
+ }