public void Parse()
{
StreamReader reader = FileUtils.GetReader(filename);
string line;
string header = null;
DnaSequence sequence = new DnaSequence();
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith(">"))
{
if (header != null)
{
process(header, sequence);
}
header = line.Substring(1);
sequence = new DnaSequence();
}
else
{
string s = StringUtils.RemoveWhitespace(line.Trim()).ToUpper();
s = s.Replace('U', 'T');
sequence.Append(s);
}
}
if (header != null)
{
process(header, sequence);
}
reader.Close();
}
public void Parse()
{
StreamReader reader = FileUtils.GetReader(filename);
string line;
string header = null;
DnaSequence sequence = new DnaSequence();
while ((line = reader.ReadLine()) != null){
if (line.StartsWith(">")){
if (header != null){
process(header, sequence);
}
header = line.Substring(1);
sequence = new DnaSequence();
} else{
string s = StringUtils.RemoveWhitespace(line.Trim()).ToUpper();
s = s.Replace('U', 'T');
sequence.Append(s);
}
}
if (header != null){
process(header, sequence);
}
reader.Close();
}