X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=eachgapignore.h;fp=eachgapignore.h;h=2e7fbd6bd228d3ed625cd1904ecd7d15075d9234;hp=0000000000000000000000000000000000000000;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a

diff --git a/eachgapignore.h b/eachgapignore.h
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+#ifndef EACHGAPIGNORE_H
+#define EACHGAPIGNORE_H
+/*
+ *  eachgapignore.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 5/7/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+ 
+ 
+#include "dist.h"
+
+/**************************************************************************************************/
+
+class eachGapIgnoreTermGapDist : public Dist {
+	
+public:
+	eachGapIgnoreTermGapDist() {}
+	eachGapIgnoreTermGapDist(const eachGapIgnoreTermGapDist& ddb) {}
+	
+	void calcDist(Sequence A, Sequence B){		
+		int diff = 0;
+		int length = 0;
+		int start = 0;
+		int end = 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] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
+				start = i;
+//				cout << "start: " << start << endl;
+				overlap = true;
+				break;
+			}
+		}
+		for(int i=alignLength-1;i>=0;i--){
+			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
+				end = i;
+//				cout << "end: " << end << endl;
+				overlap = true;
+				break;
+			}
+		}
+		
+		for(int i=start;i<=end;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
+
+