X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastalign.cpp;fp=blastalign.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=bb7192ad498c405fc476ae722db2478fa1b407ab;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/blastalign.cpp b/blastalign.cpp
deleted file mode 100644
index bb7192a..0000000
--- a/blastalign.cpp
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
- *  blastalign.cpp
- *  
- *
- *  Created by Pat Schloss on 12/16/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *	This is a basic alignment method that gets the blast program to do the heavy lifting.  In the future, we should
- *	probably incorporate NCBI's library so that we don't have to call on a user-supplied executable.  This is a child
- *	of the Alignment class, which requires a constructor and align method.
- *
- */
-
-
-#include "alignment.hpp"
-#include "blastalign.hpp"
-
-
-//**************************************************************************************************/
-
-BlastAlignment::BlastAlignment(float go, float ge, float ma, float mm) : 
-			match(ma),				//	This is the score to award for two nucleotides matching (match >= 0)
-			mismatch(mm)			//	This is the penalty to assess for a mismatch (mismatch <= 0)
-{
-	path = m->argv;
-	path = path.substr(0, (path.find_last_of('m')));
-	
-	gapOpen = abs(go);				//	This is the penalty to assess for opening a gap (gapOpen >= 0)
-	gapExtend = abs(ge);				//	This is the penalty to assess for extending a gap (gapExtend >= 0)
-		
-	int randNumber = rand();
-	candidateFileName = toString(randNumber) + ".candidate";
-	templateFileName = toString(randNumber) + ".template";
-	blastFileName = toString(randNumber) + ".pairwise";
-}
-
-//**************************************************************************************************/
-
-BlastAlignment::~BlastAlignment(){		//	The desctructor should clean up by removing the temporary 
-	m->mothurRemove(candidateFileName);	//	files used to run bl2seq
-	m->mothurRemove(templateFileName);
-	m->mothurRemove(blastFileName);
-}
-
-//**************************************************************************************************/
-
-void BlastAlignment::align(string seqA, string seqB){	//Use blastn to align the two sequences
-
-	ofstream candidateFile(candidateFileName.c_str());	//	Write the sequence to be aligned to a temporary candidate seq file
-	candidateFile << ">candidate" << endl << seqA << endl;
-	candidateFile.close();
-	
-	ofstream templateFile(templateFileName.c_str());	//	Write the unaligned template sequence to a temporary candidate seq file
-	templateFile << ">template" << endl << seqB << endl;
-	templateFile.close();
-	
-	//	The blastCommand assumes that we have DNA sequences (blastn) and that they are fairly similar (-e 0.001) and
-	//	that we don't want to apply any kind of complexity filtering (-F F)
-	string blastCommand = path + "blast/bin/bl2seq -p blastn -i " + candidateFileName + " -j " + templateFileName + " -e 0.0001 -F F -o " + blastFileName + " -W 11";
-	blastCommand += " -r " + toString(match) + " -q " + toString(mismatch);
-	blastCommand +=	" -G " + toString(gapOpen) + " -E " + toString(gapExtend);
-	
-	system(blastCommand.c_str());	//	Here we assume that "bl2seq" is in the users path or in the same folder as
-									//	this executable
-	setPairwiseSeqs();
-}
-
-/**************************************************************************************************/
-
-void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast generated alignment
-															//	to the pairwise entry in the Sequence class for the 
-															//	candidate and template Sequence objects
-	ifstream blastFile;
-	m->openInputFile(blastFileName, blastFile);
-	
-	seqAaln = "";
-	seqBaln = "";
-	
-	int candidateLength, templateLength;
-	char d;
-	
-	string candidateName, templateName;
-	
-	while((d=blastFile.get()) != '='){}
-	blastFile >> candidateName;					//	Get the candidate sequence name from flatfile
-	
-	while((d=blastFile.get()) != '('){}
-	blastFile >> candidateLength;				//	Get the candidate sequence length from flatfile
-	
-	while((d=blastFile.get())){
-		if(d == '>'){
-			blastFile >> templateName;			//	Get the template sequence name from flatfile
-			break;
-		}
-		else if(d == '*'){									//	We go here if there is no significant match
-			
-			seqAstart = 0;
-			seqBstart = 0;
-			seqAend = 0;
-			seqBend = 0;
-			pairwiseLength = 0;
-			
-//			string dummy;
-//			while(dummy != "query:"){	m->mothurOut(dummy, ""); m->mothurOutEndLine(); blastFile >> dummy;	}
-//			blastFile >> seqBend;
-//			m->mothurOut(toString(seqBend), ""); m->mothurOutEndLine();
-//			for(int i=0;i<seqBend;i++){
-//				seqAaln += 'Z';
-//				seqBaln += 'X';
-//			}
-//			pairwiseLength = 0;
-			return;
-		}
-	}
-	
-	while((d=blastFile.get()) != '='){}
-	blastFile >> templateLength;				//	Get the template sequence length from flatfile
-		
-	while((d=blastFile.get()) != 'Q'){}			//	Suck up everything else until we get to the start of the alignment
-	int queryStart, sbjctStart, queryEnd, sbjctEnd;
-	string queryLabel, sbjctLabel, query, sbjct;
-
-	blastFile >> queryLabel;	queryLabel = 'Q' + queryLabel;
-
-	
-	while(queryLabel == "Query:"){
-		blastFile >> queryStart >> query >> queryEnd;
-		
-		while((d=blastFile.get()) != 'S'){};
-		
-		blastFile >> sbjctLabel >> sbjctStart >> sbjct >> sbjctEnd;
-		
-		if(seqAaln == ""){
-			seqAstart = queryStart;
-			seqBstart = sbjctStart;
-		}
-
-		seqAaln += query;					//	concatenate each line of the sequence to what we already have
-		seqBaln += sbjct;					//	for the query and template (subject) sequence
-		
-		blastFile >> queryLabel;
-	}
-	seqAend = queryEnd;
-	seqBend = sbjctEnd;
-	pairwiseLength = seqAaln.length();
-
-	for(int i=1;i<seqBstart;i++){				//	Since the alignments don't always start at (1, 1), we need to pad
-		seqAaln = 'Z' + seqAaln;				//	the sequences so that they start at the same point
-		seqBaln = 'X' + seqBaln;
-	}
-	
-	for(int i=seqBend+1;i<=templateLength;i++){	//	since the sequences don't necessarily end at the same point, we
-		seqAaln += 'Z';							//	again need ot pad the sequences so that they extend to the length
-		seqBaln += 'X';							//	of the template sequence
-	}
-	blastFile.close();
-}
-
-//**************************************************************************************************/