SequenceDB::SequenceDB(ifstream& filehandle) {
try{
- string name, sequence, line;
- sequence = "";
- int c;
- string temp;
-
-
+
//read through file
- while ((c = filehandle.get()) != EOF) {
- name = ""; sequence = "";
- //is this a name
- if (c == '>') {
- name = readName(filehandle);
- sequence = readSequence(filehandle);
- }else { mothurOut("Error fasta in your file. Please correct."); mothurOutEndLine(); }
-
+ while (!filehandle.eof()) {
//input sequence info into sequencedb
- Sequence newSequence(name, sequence);
+ Sequence newSequence(filehandle);
data.push_back(newSequence);
//takes care of white space