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

[mothur.git] / eachgapdist.h

diff --git a/eachgapdist.h b/eachgapdist.h
deleted file mode 100644 (file)
index 1aca10c..0000000
--- a/eachgapdist.h
+++ /dev/null
@@ -1,60 +0,0 @@
-#ifndef EACHGAPDIST_H
-#define EACHGAPDIST_H
-/*
- *  eachgapdist.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 5/7/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-
-#include "dist.h"
-
-/**************************************************************************************************/
-
-class eachGapDist : public Dist {
-       
-public:
-       
-       eachGapDist() {}
-       
-       void calcDist(Sequence A, Sequence B){          
-               int diff = 0;
-               int length = 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] == '.'){
-                               break;  
-                       }
-                       else if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.') || (seqA[i] == '.' && seqB[i] == '-')){;}
-                       else{
-                               if(seqA[i] != seqB[i]){
-                                       diff++;
-                               }
-                               length++;
-                       }
-               }
-               
-               if(length == 0) {       dist = 1.0000;                                                          }
-               else                    {       dist = ((double)diff  / (double)length);        }
-       }
-};
-
-/**************************************************************************************************/
-
-#endif