X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ignoregaps.h;fp=ignoregaps.h;h=8127b6205e42d18516561565e8a4eb29ccd56ab6;hb=3117b1c3109121dff476997d3c5db5b47a77729b;hp=0000000000000000000000000000000000000000;hpb=a5a908953ab2ebb9386a895e5ddddf0135ad1f99;p=mothur.git

diff --git a/ignoregaps.h b/ignoregaps.h
new file mode 100644
index 0000000..8127b62
--- /dev/null
+++ b/ignoregaps.h
@@ -0,0 +1,67 @@
+#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:
+	
+	void calcDist(Sequence A, Sequence B){		
+		int diff = 0;
+		int length = 0;
+		int start = 0;
+		int end = 0;
+		
+		for(int i=0;i<A.getLength();i++){
+			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
+			}
+			else{
+				start = i;
+				break;
+			}
+		}
+		for(int i=A.getLength()-1;i>=0;i--){
+			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
+			}
+			else{
+				end = i;
+				break;
+			}
+		}
+		
+		for(int i=start; i<=end; i++){
+			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.'){
+				break;
+			}
+			else if((A.getAligned()[i] != '-' && B.getAligned()[i] != '-')){
+				if(A.getAligned()[i] != B.getAligned()[i]){
+					diff++;
+				}
+				length++;
+			}
+		}
+		
+		if(length == 0)		{	dist = 1.0000;								}
+		else				{	dist = ((double)diff  / (double)length);	}
+		
+	}
+	
+};
+
+/**************************************************************************************************/
+#endif
+