finished sub.sample command

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index fd9459c0d49d005437464463e421bdd61c7db3d7..f76d9826ee0224cb63d3520a30a0f7b100a5cecf 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){
@@ -57,11 +57,45 @@ QualityScores::QualityScores(ifstream& qFile, int l){
                
                //seqLength = qScores.size();   
                
+               /*while(!in.eof()){     
+                       string saveName = "";
+                       string name = "";
+                       string scores = "";
+                       
+                       in >> name; 
+                       //cout << name << endl;         
+                       if (name.length() != 0) { 
+                               saveName = name.substr(1);
+                               while (!in.eof())       {       
+                                       char c = in.get(); 
+                                       if (c == 10 || c == 13){        break;  }
+                                       else { name += c; }     
+                               } 
+                               m->gobble(in);
+                       }
+                       
+                       while(in){
+                               char letter= in.get();
+                               if(letter == '>'){      in.putback(letter);     break;  }
+                               else{ scores += letter; }
+                       }
+                       
+                //istringstream iss (scores,istringstream::in);
+                
+                //int count = 0; int tempScore;
+                //while (iss) { iss >> tempScore; count++; }
+                //cout << saveName << '\t' << count << endl;   
+                       
+                       m->gobble(in);
+               }*/             
+               
+               
+               
                for(int i=0;i<seqLength;i++){
                        qFile >> score;
                        qScores.push_back(score);
                }
-               gobble(qFile);
+               m->gobble(qFile);
 
        }
        catch(exception& e) {
@@ -70,6 +104,7 @@ QualityScores::QualityScores(ifstream& qFile, int l){
        }                                                       
 
 }
+/**************************************************************************************************/
 
 /**************************************************************************************************/