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[mothur.git] / eachgapdistignorens.h

diff --git a/eachgapdistignorens.h 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