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[mothur.git] / onegapdist.h

diff --git a/onegapdist.h b/onegapdist.h
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+#ifndef ONEGAPDIST_H
+#define ONEGAPDIST_H
+/*
+ *  onegapdist.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 5/7/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "dist.h"
+
+
+/**************************************************************************************************/
+
+class oneGapDist : public Dist {
+       
+public:
+       
+       oneGapDist() {}
+       
+       void calcDist(Sequence A, Sequence B){
+               
+               int difference = 0;
+               int minLength = 0;
+               int openGapA = 0;
+               int openGapB = 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] == '-') || (seqA[i] == '.' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.')){     ;       }
+                       else if(seqA[i] == '.' && seqB[i] == '.'){
+                               break;
+                       }
+                       else if(seqB[i] != '-' && (seqA[i] == '-' || seqA[i] == '.')){
+                               if(openGapA == 0){
+                                       difference++;
+                                       minLength++;
+                                       openGapA = 1;
+                                       openGapB = 0;
+                               }
+                       }
+                       else if(seqA[i] != '-' && (seqB[i] == '-' || seqB[i] == '.')){
+                               if(openGapB == 0){
+                                       difference++;
+                                       minLength++;
+                                       openGapA = 0;
+                                       openGapB = 1;
+                               }
+                       }
+                       else if(seqA[i] != '-' && seqB[i] != '-'){
+                               if(seqA[i] != seqB[i]){
+                                       difference++;
+                                       minLength++;
+                                       openGapA = 0;
+                                       openGapB = 0;
+                               }
+                               else{
+                                       minLength++;
+                                       openGapA = 0;
+                                       openGapB = 0;
+                               }
+                       }
+               }
+       
+               if(minLength == 0)      {       dist = 1.0000;                                                  }
+               else                            {       dist = (double)difference / minLength;  }
+       }
+       
+};
+
+/**************************************************************************************************/
+
+#endif