X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=blastalign.cpp;h=bb7192ad498c405fc476ae722db2478fa1b407ab;hp=0645fb031f0d2a4e98b4caba5695f30ecd555474;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/blastalign.cpp b/blastalign.cpp
index 0645fb0..bb7192a 100644
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -18,12 +18,11 @@
 
 //**************************************************************************************************/
 
-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)
 {
-	globaldata = GlobalData::getInstance();
-	path = globaldata->argv;
+	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)
@@ -38,9 +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);
 }
 
 //**************************************************************************************************/
@@ -72,7 +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 = "";
@@ -82,13 +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;
@@ -102,9 +101,9 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 			pairwiseLength = 0;
 			
 //			string dummy;
-//			while(dummy != "query:"){	mothurOut(dummy, ""); mothurOutEndLine(); blastFile >> dummy;	}
+//			while(dummy != "query:"){	m->mothurOut(dummy, ""); m->mothurOutEndLine(); blastFile >> dummy;	}
 //			blastFile >> seqBend;
-//			mothurOut(toString(seqBend), ""); mothurOutEndLine();
+//			m->mothurOut(toString(seqBend), ""); m->mothurOutEndLine();
 //			for(int i=0;i<seqBend;i++){
 //				seqAaln += 'Z';
 //				seqBaln += 'X';
@@ -114,10 +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;
 
@@ -127,7 +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;