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+#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
+