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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);
+	}
+
+}
+
+/**************************************************************************************************/
+