--- /dev/null
+#ifndef IGNOREGAPS_H
+#define IGNOREGAPS_H
+/*
+ * ignoregaps.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 5/7/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "dist.h"
+
+/**************************************************************************************************/
+
+// this class calculates distances by ignoring all gap characters. so if seq a has an "A" and seq
+// b has a '-', there is no penalty
+
+class ignoreGaps : public Dist {
+
+public:
+
+ ignoreGaps() {}
+
+ void calcDist(Sequence A, Sequence B){
+ int diff = 0;
+ int length = 0;
+ int start = 0;
+ bool overlap = false;
+
+ string seqA = A.getAligned();
+ string seqB = B.getAligned();
+ int alignLength = seqA.length();
+
+ for(int i=0;i<alignLength;i++){
+ if(seqA[i] != '.' && seqB[i] != '.'){
+ start = i;
+ overlap = true;
+ break;
+ }
+ }
+
+ for(int i=start; i<alignLength; i++){
+ if(seqA[i] == '.' || seqB[i] == '.'){
+ break;
+ }
+ else if((seqA[i] != '-' && seqB[i] != '-')){
+ if(seqA[i] != seqB[i]){
+ diff++;
+ }
+ length++;
+ }
+ }
+
+ //non-overlapping sequences
+ if (!overlap) { length = 0; }
+
+ if(length == 0) { dist = 1.0000; }
+ else { dist = ((double)diff / (double)length); }
+
+ }
+
+};
+
+/**************************************************************************************************/
+#endif
+