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diff --git a/needlemanoverlap.cpp b/needlemanoverlap.cpp
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-/*
- *  needleman.cpp
- *  
- *
- *  Created by Pat Schloss on 12/15/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *	This class is an Alignment child class that implements the Gotoh pairwise alignment algorithm as described in:
- *		
- *		Gotoh O. 1982.  An improved algorithm for matching biological sequences.  J. Mol. Biol.  162:705-8.
- *		Myers, EW & Miller, W.  1988.  Optimal alignments in linear space.  Comput Appl Biosci. 4:11-7.
- *
- *	This method is nice because it allows for an affine gap penalty to be assessed, which is analogous to what is used
- *	in blast and is an alternative to Needleman-Wunsch, which only charges the same penalty for each gap position.
- *	Because this method typically has problems at the ends when two sequences do not full overlap, we employ a separate
- *	method to fix the ends (see Overlap class documentation)
- *
- */
-
-#include "alignmentcell.hpp"
-#include "alignment.hpp"
-#include "overlap.hpp"
-#include "needlemanoverlap.hpp"
-
-/**************************************************************************************************/
-
-NeedlemanOverlap::NeedlemanOverlap(float gO, float f, float mm, int r) ://	note that we don't have a gap extend
-gap(gO), match(f), mismatch(mm), Alignment(r) {							//	the gap openning penalty is assessed for
-	try {																	//	every gapped position
-		for(int i=1;i<nCols;i++){
-			alignment[0][i].prevCell = 'l';					//	initialize first row by pointing all poiters to the left
-			alignment[0][i].cValue = 0;						//	and the score to zero
-		}
-		
-		for(int i=1;i<nRows;i++){
-			alignment[i][0].prevCell = 'u';					//	initialize first column by pointing all poiters upwards
-			alignment[i][0].cValue = 0;						//	and the score to zero
-		}
-	
-	}
-	catch(exception& e) {
-		m->errorOut(e, "NeedlemanOverlap", "NeedlemanOverlap");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-NeedlemanOverlap::~NeedlemanOverlap(){	/*	do nothing	*/	}
-
-/**************************************************************************************************/
-
-void NeedlemanOverlap::align(string A, string B){
-	try {
-	
-		seqA = ' ' + A;	lA = seqA.length();		//	algorithm requires a dummy space at the beginning of each string
-		seqB = ' ' + B;	lB = seqB.length();		//	algorithm requires a dummy space at the beginning of each string
-
-		if (lA > nRows) { m->mothurOut("One of your candidate sequences is longer than you longest template sequence. Your longest template sequence is " + toString(nRows) + ". Your candidate is " + toString(lA) + "."); m->mothurOutEndLine();  }
-		
-		for(int i=1;i<lB;i++){					//	This code was largely translated from Perl code provided in Ex 3.1 
-		
-			for(int j=1;j<lA;j++){				//	of the O'Reilly BLAST book.  I found that the example output had a
-	
-				//	number of errors
-				float diagonal;
-				if(seqB[i] == seqA[j])	{	diagonal = alignment[i-1][j-1].cValue + match;		}
-				else					{	diagonal = alignment[i-1][j-1].cValue + mismatch;	}
-			
-				float up	= alignment[i-1][j].cValue + gap;
-				float left	= alignment[i][j-1].cValue + gap;
-				
-				if(diagonal >= up){
-					if(diagonal >= left){
-						alignment[i][j].cValue = diagonal;
-						alignment[i][j].prevCell = 'd';
-					}
-					else{
-						alignment[i][j].cValue = left;
-						alignment[i][j].prevCell = 'l';
-					}
-				}
-				else{
-					if(up >= left){
-						alignment[i][j].cValue = up;
-						alignment[i][j].prevCell = 'u';
-					}
-					else{
-						alignment[i][j].cValue = left;
-						alignment[i][j].prevCell = 'l';
-					}
-				}
-			}
-		}
-
-		Overlap over;						
-		over.setOverlap(alignment, lA, lB, 0);		//	Fix gaps at the beginning and end of the sequences
-		traceBack();								//	Traceback the alignment to populate seqAaln and seqBaln
-	
-	}
-	catch(exception& e) {
-		m->errorOut(e, "NeedlemanOverlap", "align");
-		exit(1);
-	}
-
-}
-
-/**************************************************************************************************/
-