X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignment.cpp;fp=alignment.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=235216e8e59c82be596004559445c021312acb40;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/alignment.cpp b/alignment.cpp
deleted file mode 100644
index 235216e..0000000
--- a/alignment.cpp
+++ /dev/null
@@ -1,196 +0,0 @@
-/*
- *  alignment.cpp
- *
- *  Created by Pat Schloss on 12/15/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *  This is a class for an abstract datatype for classes that implement various types of alignment	algorithms.
- *	As of 12/18/08 these included alignments based on blastn, needleman-wunsch, and the	Gotoh algorithms
- *  
- */
-
-#include "alignmentcell.hpp"
-#include "alignment.hpp"
-
-
-/**************************************************************************************************/
-
-Alignment::Alignment() {	/*	do nothing	*/	}
-
-/**************************************************************************************************/
-
-Alignment::Alignment(int A) : nCols(A), nRows(A) {
-	try {
- 
-		m = MothurOut::getInstance();
-		alignment.resize(nRows);			//	For the Gotoh and Needleman-Wunsch we initialize the dynamic programming
-		for(int i=0;i<nRows;i++){			//	matrix by initializing a matrix that is A x A.  By default we will set A
-			alignment[i].resize(nCols);		//	at 2000 for 16S rRNA gene sequences
-		}	
-	}
-	catch(exception& e) {
-		m->errorOut(e, "Alignment", "Alignment");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-void Alignment::resize(int A) {
-	try {
-		nCols = A;
-		nRows = A;
-
-		alignment.resize(nRows);			
-		for(int i=0;i<nRows;i++){			
-			alignment[i].resize(nCols);		
-		}	
-	}
-	catch(exception& e) {
-		m->errorOut(e, "Alignment", "resize");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-void Alignment::traceBack(){			//	This traceback routine is used by the dynamic programming algorithms
-	try {	
-									//	to fill the values of seqAaln and seqBaln
-		seqAaln = "";
-		seqBaln = "";
-		int row = lB-1;
-		int column = lA-1;
-		//	seqAstart = 1;
-		//	seqAend = column;
-		
-		AlignmentCell currentCell = alignment[row][column];	//	Start the traceback from the bottom-right corner of the
-		//	matrix
-		
-		if(currentCell.prevCell == 'x'){	seqAaln = seqBaln = "NOALIGNMENT";		}//If there's an 'x' in the bottom-
-		else{												//	right corner bail out because it means nothing got aligned
-			while(currentCell.prevCell != 'x'){				//	while the previous cell isn't an 'x', keep going...
-				
-				if(currentCell.prevCell == 'u'){			//	if the pointer to the previous cell is 'u', go up in the
-					seqAaln = '-' + seqAaln;				//	matrix.  this indicates that we need to insert a gap in
-					seqBaln = seqB[row] + seqBaln;			//	seqA and a base in seqB
-					currentCell = alignment[--row][column];
-				}
-				else if(currentCell.prevCell == 'l'){		//	if the pointer to the previous cell is 'l', go to the left
-					seqBaln = '-' + seqBaln;				//	in the matrix.  this indicates that we need to insert a gap
-					seqAaln = seqA[column] + seqAaln;		//	in seqB and a base in seqA
-					currentCell = alignment[row][--column];
-				}
-				else{
-					seqAaln = seqA[column] + seqAaln;		//	otherwise we need to go diagonally up and to the left,
-					seqBaln = seqB[row] + seqBaln;			//	here we add a base to both alignments
-					currentCell = alignment[--row][--column];
-				}
-			}
-		}
-		
-		pairwiseLength = seqAaln.length();
-		seqAstart = 1;	seqAend = 0;
-		seqBstart = 1;	seqBend = 0;
-		
-		for(int i=0;i<seqAaln.length();i++){
-			if(seqAaln[i] != '-' && seqBaln[i] == '-')		{	seqAstart++;	}
-			else if(seqAaln[i] == '-' && seqBaln[i] != '-')	{	seqBstart++;	}
-			else											{	break;			}
-		}
-		
-		pairwiseLength -= (seqAstart + seqBstart - 2);
-		
-		for(int i=seqAaln.length()-1; i>=0;i--){
-			if(seqAaln[i] != '-' && seqBaln[i] == '-')		{	seqAend++;		}
-			else if(seqAaln[i] == '-' && seqBaln[i] != '-')	{	seqBend++;		}
-			else											{	break;			}
-		}
-		pairwiseLength -= (seqAend + seqBend);
-		
-		seqAend = seqA.length() - seqAend - 1;
-		seqBend = seqB.length() - seqBend - 1;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "Alignment", "traceBack");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-Alignment::~Alignment(){
-	try {
-		for (int i = 0; i < alignment.size(); i++) {
-			for (int j = (alignment[i].size()-1); j >= 0; j--) {  alignment[i].pop_back();  }
-		}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "Alignment", "~Alignment");
-		exit(1);
-	}
-}
-
-/**************************************************************************************************/
-
-string Alignment::getSeqAAln(){
-	return seqAaln;										//	this is called to get the alignment of seqA
-}
-
-/**************************************************************************************************/
-
-string Alignment::getSeqBAln(){
-	return seqBaln;										//	this is called to get the alignment of seqB							
-}
-
-/**************************************************************************************************/
-
-int Alignment::getCandidateStartPos(){
-	return seqAstart;									//	this is called to report the quality of the alignment
-}
-
-/**************************************************************************************************/
-
-int Alignment::getCandidateEndPos(){
-	return seqAend;										//	this is called to report the quality of the alignment
-}
-
-/**************************************************************************************************/
-
-int Alignment::getTemplateStartPos(){
-	return seqBstart;									//	this is called to report the quality of the alignment
-}
-
-/**************************************************************************************************/
-
-int Alignment::getTemplateEndPos(){
-	return seqBend;										//	this is called to report the quality of the alignment
-}
-
-/**************************************************************************************************/
-
-int Alignment::getPairwiseLength(){
-	return pairwiseLength;								//	this is the pairwise alignment length
-}
-
-/**************************************************************************************************/
-
-//int Alignment::getLongestTemplateGap(){
-//
-//	int length = seqBaln.length();
-//	int longGap = 0;
-//	int gapLength = 0;
-//	
-//	int start = seqAstart;
-//	if(seqAstart < seqBstart){	start = seqBstart;	}
-//	for(int i=seqAstart;i<length;i++){
-//		if(seqBaln[i] == '-'){
-//			gapLength++;
-//		}
-//		else{
-//			if(gapLength > 0){
-//				if(gapLength > longGap){	longGap = gapLength;	}
-//			}
-//			gapLength = 0;
-//		}
-//	}
-//	return longGap;
-//}
-
-/**************************************************************************************************/