Revert to previous commit

[mothur.git] / onegapignore.h

diff --git a/onegapignore.h b/onegapignore.h
new file mode 100644 (file)
index 0000000..fdbc196
--- /dev/null
+++ b/onegapignore.h
@@ -0,0 +1,95 @@
+#ifndef ONEIGNOREGAPS_H
+#define ONEIGNOREGAPS_H
+/*
+ *  onegapignore.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 5/7/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "dist.h"
+
+/**************************************************************************************************/
+
+class oneGapIgnoreTermGapDist : public Dist {
+       
+public:
+       
+       oneGapIgnoreTermGapDist() {}
+       
+       void calcDist(Sequence A, Sequence B){
+               
+               int difference = 0;
+               int openGapA = 0;
+               int openGapB = 0;
+               int minLength = 0;
+               int start = 0;
+               int end = 0;
+               bool overlap = false;
+               
+               string seqA = A.getAligned();
+               string seqB = B.getAligned();
+               int alignLength = seqA.length();
+
+               // this assumes that sequences start and end with '.'s instead of'-'s.
+               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] == '-'){   ;       }
+                       else if(seqB[i] != '-' && seqA[i] == '-'){
+                               if(openGapA == 0){
+                                       difference++;
+                                       minLength++;
+                                       openGapA = 1;
+                                       openGapB = 0;
+                               }
+                       }
+                       else if(seqA[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;
+                       }
+               }
+               
+               //non-overlapping sequences
+               if (!overlap) { minLength = 0; }
+               
+               if(minLength == 0)      {       dist = 1.0000;                                                  }
+               else                            {       dist = (double)difference / minLength;  }
+       }
+
+};
+
+/**************************************************************************************************/
+
+#endif
+