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

[mothur.git] / eachgapignore.h

diff --git a/eachgapignore.h b/eachgapignore.h
deleted file mode 100644 (file)
index 2e7fbd6..0000000
--- a/eachgapignore.h
+++ /dev/null
@@ -1,77 +0,0 @@
-#ifndef EACHGAPIGNORE_H
-#define EACHGAPIGNORE_H
-/*
- *  eachgapignore.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 5/7/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
- 
- 
-#include "dist.h"
-
-/**************************************************************************************************/
-
-class eachGapIgnoreTermGapDist : public Dist {
-       
-public:
-       eachGapIgnoreTermGapDist() {}
-       eachGapIgnoreTermGapDist(const eachGapIgnoreTermGapDist& ddb) {}
-       
-       void calcDist(Sequence A, Sequence B){          
-               int diff = 0;
-               int length = 0;
-               int start = 0;
-               int end = 0;
-               bool overlap = false;
-               
-               string seqA = A.getAligned();
-               string seqB = B.getAligned();
-               int alignLength = seqA.length();
-               
-               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] == '.'){
-                               break;  
-                       }
-                       else if(seqA[i] != '-' || seqB[i] != '-'){
-                               if(seqA[i] != seqB[i]){
-                                       diff++;
-                               }
-                               length++;
-                       }
-               }
-               
-               //non-overlapping sequences
-               if (!overlap) { length = 0; }
-               
-               if(length == 0) {       dist = 1.0000;                                                          }
-               else                    {       dist = ((double)diff  / (double)length);        }
-               
-       }
-       
-};
-
-/**************************************************************************************************/
-
-#endif
-
-