X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=eachgapdistignorens.h;fp=eachgapdistignorens.h;h=9605a009aac07bab90992d355499d1bc818b9be7;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/eachgapdistignorens.h b/eachgapdistignorens.h
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+++ b/eachgapdistignorens.h
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+#ifndef EACHGAPDISTIGNORENS_H
+#define EACHGAPDISTIGNORENS_H
+
+/*
+ *  eachgapdistignorens.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 4/20/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "dist.h"
+
+/**************************************************************************************************/
+
+class eachGapDistIgnoreNs : public Dist {
+	
+public:
+	void calcDist(Sequence A, Sequence B){		
+		int diff = 0;
+		int length = 0;
+		int start = 0;
+		
+		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;
+				break;
+			}
+		}
+		
+		for(int i=start;i<alignLength;i++){
+			if(seqA[i] == '.' && seqB[i] == '.'){
+				break;	
+			}
+			else if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.') || (seqA[i] == '.' && seqB[i] == '-') || seqA[i] == 'N' || seqB[i] == 'N'){;}
+			else{
+				if(seqA[i] != seqB[i]){
+					diff++;
+				}
+				length++;
+			}
+		}
+		
+		if(length == 0)	{	dist = 1.0000;								}
+		else			{	dist = ((double)diff  / (double)length);	}
+	}
+};
+
+/**************************************************************************************************/
+
+#endif