X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastalign.cpp;h=624210f5f977ac505a32119e574561ec7e92dcc2;hb=28d65de5f06f5b033109a3b8bbb6d3c4060914d3;hp=e4d5e8ac039d60f9f1352d6408121246f9d9864d;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;p=mothur.git

diff --git a/blastalign.cpp b/blastalign.cpp
index e4d5e8a..624210f 100644
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -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:"){	cout << dummy << endl;blastFile >> dummy;	}
+//			while(dummy != "query:"){	mothurOut(dummy, ""); mothurOutEndLine(); blastFile >> dummy;	}
 //			blastFile >> seqBend;
-//			cout << seqBend << endl;
+//			mothurOut(toString(seqBend), ""); 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;
 		
@@ -154,6 +154,7 @@ 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();
 }
 
 //**************************************************************************************************/