moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / onegapdist.h

diff --git a/onegapdist.h b/onegapdist.h
deleted file mode 100644 (file)
index 3e5b6c7..0000000
--- a/onegapdist.h
+++ /dev/null
@@ -1,86 +0,0 @@
-#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