public override List <NamedSequence> Parse(TextReader reader)
{
List <NamedSequence> seqs = new List <NamedSequence>();
string line;
//string name = null;
NamedSequence seqToAdd = null;
StringBuilder sequence = new StringBuilder();
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith(">"))
{
if (seqToAdd != null)
{
//seqs.Add(new NamedSequence(name, RemoveWhiteSpace(sequence.ToString())));
seqToAdd.Sequence = sequence.ToString();
seqs.Add(seqToAdd);
}
seqToAdd = NamedSequence.Parse(line.Substring(1).Trim());
//name = line.Substring(1).Trim();
sequence = new StringBuilder(sequence.Length);
}
else
{
sequence.Append(line.Trim());
}
}
//seqs.Add(new NamedSequence(name, RemoveWhiteSpace(sequence.ToString())));
seqToAdd.Sequence = sequence.ToString();
seqs.Add(seqToAdd);
return(seqs);
}
public override List <NamedSequence> Parse(TextReader reader)
{
if (NoHeader)
{
reader = new StringReader(OUTPUT_HEADER + "\n" + reader.ReadToEnd());
}
List <NamedSequence> seqs = new List <NamedSequence>();
string[] header = null;
foreach (Dictionary <string, string> row in SpecialFunctions.TabFileTable(reader, "", true, false, true))
{
if (header == null)
{
header = row[""].Split('\t');
Helper.CheckCondition(header.Length == 2, "Header does not conform to tab file format: " + row[""]);
continue;
}
string name = row[header[0]];
string seq = row[header[1]];
NamedSequence namedSeq = NamedSequence.Parse(name);
namedSeq.Sequence = RemoveWhiteSpace(seq);
seqs.Add(namedSeq);
}
return(seqs);
}
public override List <NamedSequence> Parse(TextReader reader)
{
string line;
string[] fields;
line = reader.ReadLine().Trim();
if (!ConformsToFileFormat(line))
{
throw new FormatException("File does not conform to Phylip format. First line must be two integers specifying number of sequences and sequence length.");
}
fields = Regex.Split(line, @"\s+");
int lineCount, lineLength;
try
{
lineCount = int.Parse(fields[0]);
lineLength = int.Parse(fields[1]);
}
catch (FormatException e)
{
Console.WriteLine("Error parsing Phylip header: {0} split to {1} and {2}", line, fields[0], fields[1]);
throw e;
}
List <NamedSequence> seqs = new List <NamedSequence>(lineCount);
while ((line = reader.ReadLine()) != null)
{
if (!string.IsNullOrWhiteSpace(line))
{
int endOfName = Math.Max(10, line.IndexOfAny(new char[] { ' ', '\t' }, 0, Math.Min(50, line.Length)));
string name = line.Substring(0, endOfName).Trim();
string seq = RemoveWhiteSpace(line.Substring(endOfName));
//NamedSequence sequence = new NamedSequence(name, seq);
NamedSequence sequence = NamedSequence.Parse(name);
sequence.Sequence = seq;
if (sequence.Sequence.Length != lineLength)
{
throw new FormatException(string.Format("Expected {0} to be {1} chars long, but its {2} long.",
sequence.Name, lineLength, sequence.Sequence.Length));
}
seqs.Add(sequence);
}
}
if (seqs.Count != lineCount)
{
throw new FormatException(string.Format("Expected {0} sequences. Read {1}.", lineCount, seqs.Count));
}
return(seqs);
}
