/***********************************************************************/
-SequenceDB::SequenceDB() {}
+SequenceDB::SequenceDB() { m = MothurOut::getInstance(); }
/***********************************************************************/
//the clear function free's the memory
SequenceDB::~SequenceDB() { clear(); }
while (!filehandle.eof()) {
//input sequence info into sequencedb
Sequence newSequence(filehandle);
- data.push_back(newSequence);
+
+ if (newSequence.getName() != "") { data.push_back(newSequence); }
//takes care of white space
gobble(filehandle);
}
catch(exception& e) {
- errorOut(e, "SequenceDB", "SequenceDB");
+ m->errorOut(e, "SequenceDB", "SequenceDB");
exit(1);
}
}
return name;
}
catch(exception& e) {
- errorOut(e, "SequenceDB", "readName");
+ m->errorOut(e, "SequenceDB", "readName");
exit(1);
}
}
return sequence;
}
catch(exception& e) {
- errorOut(e, "SequenceDB", "readSequence");
+ m->errorOut(e, "SequenceDB", "readSequence");
exit(1);
}
}
data[index] = Sequence(data[index].getName(), newUnaligned);
}
catch(exception& e) {
- errorOut(e, "SequenceDB", "set");
+ m->errorOut(e, "SequenceDB", "set");
exit(1);
}
}
data[index] = newSeq;
}
catch(exception& e) {
- errorOut(e, "SequenceDB", "set");
+ m->errorOut(e, "SequenceDB", "set");
exit(1);
}
}
data.resize(newSize);
}
catch(exception& e) {
- errorOut(e, "SequenceDB", "resize");
+ m->errorOut(e, "SequenceDB", "resize");
exit(1);
}
}
data.clear();
}
catch(exception& e) {
- errorOut(e, "SequenceDB", "clear");
+ m->errorOut(e, "SequenceDB", "clear");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "SequenceDB", "print");
+ m->errorOut(e, "SequenceDB", "print");
exit(1);
}
}
data.push_back(newSequence);
}
catch(exception& e) {
- errorOut(e, "SequenceDB", "push_back");
+ m->errorOut(e, "SequenceDB", "push_back");
exit(1);
}
}