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[mothur.git] / eachgapignore.h

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
+
+