changing command name classify.shared to classifyrf.shared

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 33ca1728052e4db59372fc2d8129e5bcbaf729c5..0408b83ebaf0d79f31e5290278fa29e567c1cb87 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -32,22 +32,22 @@ QualityScores::QualityScores(ifstream& qFile){
                m = MothurOut::getInstance();
 
                int score;
-               seqName = getSequenceName(qFile);
+               seqName = getSequenceName(qFile); m->gobble(qFile);
                
         if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "'\n.");  }
         
                if (!m->control_pressed) {
-            string qScoreString = m->getline(qFile);
+            string qScoreString = m->getline(qFile); m->gobble(qFile);
             
             if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + qScoreString + "'\n.");  }
             
             while(qFile.peek() != '>' && qFile.peek() != EOF){
                 if (m->control_pressed) { break; }
-                string temp = m->getline(qFile);
+                string temp = m->getline(qFile); m->gobble(qFile);
                 if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n.");  }
                 qScoreString +=  ' ' + temp;
             }
-            //cout << "done reading " << endl; 
+            //cout << "done reading " << endl;
             istringstream qScoreStringStream(qScoreString);
             int count = 0;
             while(!qScoreStringStream.eof()){
@@ -68,7 +68,7 @@ QualityScores::QualityScores(ifstream& qFile){
         }
                
                seqLength = qScores.size();
-               //cout << "seqlength = " << seqLength << '\t' << count << endl;
+               //cout << "seqlength = " << seqLength  << endl;
                
        }
        catch(exception& e) {
@@ -89,9 +89,7 @@ string QualityScores::getSequenceName(ifstream& qFile) {
             
                        name = name.substr(1); 
             
-            for (int i = 0; i < name.length(); i++) {
-                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-            }
+            m->checkName(name);
             
         }else{ m->mothurOut("Error in reading your qfile, at position " + toString(qFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
         
@@ -106,10 +104,7 @@ string QualityScores::getSequenceName(ifstream& qFile) {
 void QualityScores::setName(string name) {
        try {
       
-        for (int i = 0; i < name.length(); i++) {
-            if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-        }     
-    
+        m->checkName(name);   
         seqName = name;
        }
        catch(exception& e) {