X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastalign.cpp;h=bb7192ad498c405fc476ae722db2478fa1b407ab;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=0a1350fac0c7fa655d5d04585156c28445c4d0d5;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/blastalign.cpp b/blastalign.cpp
index 0a1350f..bb7192a 100644
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -11,7 +11,6 @@
  *
  */
 
-using namespace std;
 
 #include "alignment.hpp"
 #include "blastalign.hpp"
@@ -19,10 +18,13 @@ using namespace std;
 
 //**************************************************************************************************/
 
-BlastAlignment::BlastAlignment(float go, float ge, float m, float mm) : 
-			match(m),				//	This is the score to award for two nucleotides matching (match >= 0)
+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)
 		
@@ -35,9 +37,9 @@ BlastAlignment::BlastAlignment(float go, float ge, float m, float mm) :
 //**************************************************************************************************/
 
 BlastAlignment::~BlastAlignment(){		//	The desctructor should clean up by removing the temporary 
-	remove(candidateFileName.c_str());	//	files used to run bl2seq
-	remove(templateFileName.c_str());
-	remove(blastFileName.c_str());
+	m->mothurRemove(candidateFileName);	//	files used to run bl2seq
+	m->mothurRemove(templateFileName);
+	m->mothurRemove(blastFileName);
 }
 
 //**************************************************************************************************/
@@ -54,7 +56,7 @@ void BlastAlignment::align(string seqA, string seqB){	//Use blastn to align the
 	
 	//	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 = "~/Pipeline/src/cpp/production/blast/bin/bl2seq -p blastn -i " + candidateFileName + " -j " + templateFileName + " -e 0.0001 -F F -o " + blastFileName + " -W 11";
+	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);
 	
@@ -69,7 +71,7 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 															//	to the pairwise entry in the Sequence class for the 
 															//	candidate and template Sequence objects
 	ifstream blastFile;
-	openInputFile(blastFileName, blastFile);
+	m->openInputFile(blastFileName, blastFile);
 	
 	seqAaln = "";
 	seqBaln = "";
@@ -79,13 +81,13 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 	
 	string candidateName, templateName;
 	
-	while(d=blastFile.get() != '='){};
+	while((d=blastFile.get()) != '='){}
 	blastFile >> candidateName;					//	Get the candidate sequence name from flatfile
 	
-	while(d=blastFile.get() != '('){};
+	while((d=blastFile.get()) != '('){}
 	blastFile >> candidateLength;				//	Get the candidate sequence length from flatfile
 	
-	while(d=blastFile.get()){
+	while((d=blastFile.get())){
 		if(d == '>'){
 			blastFile >> templateName;			//	Get the template sequence name from flatfile
 			break;
@@ -99,9 +101,9 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 			pairwiseLength = 0;
 			
 //			string dummy;
-//			while(dummy != "query:"){	cout << dummy << endl;blastFile >> dummy;	}
+//			while(dummy != "query:"){	m->mothurOut(dummy, ""); m->mothurOutEndLine(); blastFile >> dummy;	}
 //			blastFile >> seqBend;
-//			cout << seqBend << endl;
+//			m->mothurOut(toString(seqBend), ""); m->mothurOutEndLine();
 //			for(int i=0;i<seqBend;i++){
 //				seqAaln += 'Z';
 //				seqBaln += 'X';
@@ -111,10 +113,10 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 		}
 	}
 	
-	while(d=blastFile.get() != '='){};
+	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
+	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;
 
@@ -124,7 +126,7 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 	while(queryLabel == "Query:"){
 		blastFile >> queryStart >> query >> queryEnd;
 		
-		while(d=blastFile.get() != 'S'){};
+		while((d=blastFile.get()) != 'S'){};
 		
 		blastFile >> sbjctLabel >> sbjctStart >> sbjct >> sbjctEnd;
 		
@@ -151,6 +153,7 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 		seqAaln += 'Z';							//	again need ot pad the sequences so that they extend to the length
 		seqBaln += 'X';							//	of the template sequence
 	}
+	blastFile.close();
 }
 
 //**************************************************************************************************/