+ return PID(seq1, seq2, start, end, true,false);
+ }
+ /**
+ * Calculate percent identity for a pair of sequences over a particular range, with different options for ignoring gaps.
+ * @param seq1
+ * @param seq2
+ * @param start - position in seqs
+ * @param end - position in seqs
+ * @param wcGaps - if true - gaps match any character, if false, do not match anything
+ * @param ungappedOnly - if true - only count PID over ungapped columns
+ * @return
+ */
+ public final static float PID(String seq1, String seq2, int start, int end, boolean wcGaps, boolean ungappedOnly)
+ {