X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastalign.cpp;h=5e7fb61aa77e7c34ca7367393766b1a5455c9213;hb=5e5253ff472de3c6349e562d2580873287be0c65;hp=0645fb031f0d2a4e98b4caba5695f30ecd555474;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/blastalign.cpp b/blastalign.cpp
index 0645fb0..5e7fb61 100644
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -72,7 +72,7 @@ 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 +82,13 @@ 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 +102,9 @@ 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 +114,10 @@ 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 +127,7 @@ 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;