X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ignoregaps.h;fp=ignoregaps.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=894f92d9644182ece0a7d18e491384d2058f2d54;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/ignoregaps.h b/ignoregaps.h
deleted file mode 100644
index 894f92d..0000000
--- a/ignoregaps.h
+++ /dev/null
@@ -1,67 +0,0 @@
-#ifndef IGNOREGAPS_H
-#define IGNOREGAPS_H
-/*
- *  ignoregaps.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 5/7/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "dist.h"
-
-/**************************************************************************************************/
-
-//	this class calculates distances by ignoring all gap characters.  so if seq a has an "A" and seq
-//	b has a '-', there is no penalty
-
-class ignoreGaps : public Dist {
-	
-public:
-	
-	ignoreGaps() {}
-	
-	void calcDist(Sequence A, Sequence B){		
-		int diff = 0;
-		int length = 0;
-		int start = 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] != '.'){
-				start = i;
-				overlap = true;
-				break;
-			}
-		}
-		
-		for(int i=start; i<alignLength; 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
-