X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=qualityscores.cpp;h=f76d9826ee0224cb63d3520a30a0f7b100a5cecf;hb=3a13eff5c26d6fc156a299c9fa7f5497bded94a0;hp=fd9459c0d49d005437464463e421bdd61c7db3d7;hpb=6e81846c8e5b2614f6b06643a9f558fb0e6669fa;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index fd9459c..f76d982 100644
--- 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){
 	}							
 
 }
+/**************************************************************************************************/
 
 /**************************************************************************************************/