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

[mothur.git] / onegapignore.h

diff --git a/onegapignore.h b/onegapignore.h
deleted file mode 100644 (file)
index fdbc196..0000000
--- a/onegapignore.h
+++ /dev/null
@@ -1,95 +0,0 @@
-#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
-