altered venn command to make use of sharedchao for any number of groups, fixed window...

[mothur.git] / onegapignore.h

diff --git a/onegapignore.h b/onegapignore.h
new file mode 100644 (file)
index 0000000..ee6cc52
--- /dev/null
+++ b/onegapignore.h
@@ -0,0 +1,87 @@
+#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:
+       void calcDist(Sequence A, Sequence B){
+               
+               int difference = 0;
+               int openGapA = 0;
+               int openGapB = 0;
+               int minLength = 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] == '-'){}
+                       else if(A.getAligned()[i] == '-' && B.getAligned()[i] != '-'){
+                               if(openGapA == 0){
+                                       difference++;
+                                       minLength++;
+                                       openGapA = 1;
+                                       openGapB = 0;
+                               }
+                       }
+                       else if(A.getAligned()[i] != '-' && B.getAligned()[i] == '-'){
+                               if(openGapB == 0){
+                                       difference++;
+                                       minLength++;
+                                       openGapA = 0;
+                                       openGapB = 1;
+                               }
+                       }
+                       else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
+                               if(A.getAligned()[i] != B.getAligned()[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
+