moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index fd9459c0d49d005437464463e421bdd61c7db3d7..fa78b69d653cb841c33833d6249bab6b6ecaf18c 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -35,18 +35,18 @@ QualityScores::QualityScores(ifstream& qFile, int l){
                int score;
                
                //string line;
-               //getline(qFile, line); 
+               //m->getline(qFile, line); 
                //istringstream nameStream(line);
        
                qFile >> seqName; 
                while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13 || c == -1){       break;  }       } // get rest of line 
-               gobble(qFile);
+               m->gobble(qFile);
                if (seqName == "") { m->mothurOut("Error reading quality file, name blank at position, " + toString(qFile.tellg())); m->mothurOutEndLine(); }
                else {
                        seqName = seqName.substr(1); 
                }
 
-               //getline(qFile, line);
+               //m->getline(qFile, line);
                //istringstream qualStream(line);
        
                //while(qualStream){
@@ -61,7 +61,7 @@ QualityScores::QualityScores(ifstream& qFile, int l){
                        qFile >> score;
                        qScores.push_back(score);
                }
-               gobble(qFile);
+               m->gobble(qFile);
 
        }
        catch(exception& e) {