/**************************************************************************************************/
-QualityScores::QualityScores(ifstream& qFile){
+QualityScores::QualityScores(ifstream& qFile, int l){
try {
m = MothurOut::getInstance();
seqName = "";
- seqLength = -1;
+ seqLength = l;
int score;
string line;
- getline(qFile, line);
+ getline(qFile, line); gobble(qFile);
istringstream nameStream(line);
nameStream >> seqName;
seqName = seqName.substr(1);
- getline(qFile, line);
- istringstream qualStream(line);
+ //getline(qFile, line);
+ //istringstream qualStream(line);
- while(qualStream){
- qualStream >> score;
+ //while(qualStream){
+ // qualStream >> score;
+ // qScores.push_back(score);
+ //}
+ //qScores.pop_back();
+
+ //seqLength = qScores.size();
+
+ for(int i=0;i<seqLength;i++){
+ qFile >> score;
qScores.push_back(score);
}
- qScores.pop_back();
-
- seqLength = qScores.size();
+ gobble(qFile);
+
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "QualityScores");