added stricter compilation requirements and fixed resulting errors

[mothur.git] / blastalign.cpp

diff --git a/blastalign.cpp b/blastalign.cpp
index a4773138bd6f8102acaea659291fa675ea25a6fc..624210f5f977ac505a32119e574561ec7e92dcc2 100644 (file)
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -11,7 +11,6 @@
  *
  */
 
-using namespace std;
 
 #include "alignment.hpp"
 #include "blastalign.hpp"
@@ -83,13 +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;
@@ -103,9 +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';
@@ -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;
 
@@ -128,7 +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;
                
@@ -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();
 }
 
 //**************************************************************************************************/