X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;h=3f8722f34f83416aa143f21a5a81e99c7329a7d8;hb=47af4126c6ece121172cd486c1ca7eeb1ccae2de;hp=8b8e4ec22c68ea406ddcafeee6e4a1abb280566a;hpb=6973be461c47c057531f447de22003a30cabc193;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 8b8e4ec..3f8722f 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -44,16 +44,66 @@ QualityScores::QualityScores(ifstream& qFile){
 		else{
 			seqName = seqName.substr(1);
 		}
-		
 		string qScoreString = m->getline(qFile);
+		while(qFile.peek() != '>' && qFile.peek() != EOF){
+			qScoreString += ' ' + m->getline(qFile);
+		}
 		
 		istringstream qScoreStringStream(qScoreString);
+		int count = 0;
 		while(!qScoreStringStream.eof()){
+			if (m->control_pressed) { break; }
 			qScoreStringStream >> score;
 			qScores.push_back(score);
+			count++;
 		}
 		qScores.pop_back();
+		
+//		string scores = "";
+//		
+//		while(!qFile.eof()){	
+//			
+//			qFile >> seqName; 
+//			
+//			//get name
+//			if (seqName.length() != 0) { 
+//				seqName = seqName.substr(1);
+//				while (!qFile.eof())	{	
+//					char c = qFile.get(); 
+//					//gobble junk on line
+//					if (c == 10 || c == 13){	break;	}
+//				} 
+//				m->gobble(qFile);
+//			}
+//			
+//			//get scores
+//			while(qFile){
+//				char letter=qFile.get();
+//				if((letter == '>')){	qFile.putback(letter);	break;	}
+//				else if (isprint(letter)) { scores += letter; }
+//			}
+//			m->gobble(qFile);
+//			
+//			break;
+//		}
+//		
+//		//convert scores string to qScores
+//		istringstream qScoreStringStream(scores);
+//		
+//		int score;
+//		while(!qScoreStringStream.eof()){
+//			
+//			if (m->control_pressed) { break; }
+//			
+//			qScoreStringStream >> score;
+//			qScores.push_back(score);
+//		}
+//		
+//		qScores.pop_back();
+
 		seqLength = qScores.size();
+		
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "QualityScores", "QualityScores");
@@ -101,7 +151,7 @@ void QualityScores::printQScores(ofstream& qFile){
 void QualityScores::trimQScores(int start, int end){
 	try {
 		vector<int> hold;
-		
+			
 		if(end == -1){		
 			hold = vector<int>(qScores.begin()+start, qScores.end());
 			qScores = hold;