version 1.4

[mothur.git] / blastalign.cpp

diff --git a/blastalign.cpp b/blastalign.cpp
index a4773138bd6f8102acaea659291fa675ea25a6fc..cb6abf97b8840aa32bfc4e9bf95315e30e4dbf10 100644 (file)
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -11,7 +11,6 @@
  *
  */
 
-using namespace std;
 
 #include "alignment.hpp"
 #include "blastalign.hpp"
@@ -83,10 +82,10 @@ 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()){
@@ -115,10 +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;
 
@@ -155,6 +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();
 }
 
 //**************************************************************************************************/