/// <summary>
/// Try Parse Sequence File.
/// </summary>
/// <param name="fileName">The fileName.</param>
/// <param name="alphabet">The Alphabet.</param>
/// <param name="sequences">List of sequences.</param>
/// <returns>True if Parsed sequence properly.</returns>
private static bool TryParseSequenceFile(string fileName, IAlphabet alphabet, out IList <ISequence> sequences)
{
// Read the first line.
string firstLine;
using (var reader = new StreamReader(fileName))
{
firstLine = reader.ReadLine();
}
// Attempt to discover the format.
if (ValidateFastaFormat(firstLine))
{
var parse = new FastAParser {
Alphabet = alphabet
};
using (parse.Open(fileName))
{
sequences = parse.Parse().ToList();
}
return(true);
}
if (ValidatePhylipFormat(firstLine))
{
var parse = new PhylipParser {
Alphabet = alphabet
};
using (parse.Open(fileName))
{
sequences = ConvertAlignedSequenceToSequence(parse.Parse());
}
return(true);
}
if (ValidateTabFormat(firstLine))
{
var parse = new FieldTextFileParser {
Alphabet = alphabet
};
using (parse.Open(fileName))
{
sequences = parse.Parse().ToList();
return(true);
}
}
sequences = null;
return(false);
}
/// <summary>
/// Try Parse Sequence File.
/// </summary>
/// <param name="fileName">The fileName.</param>
/// <param name="alphabet">The Alphabet.</param>
/// <param name="sequences">List of sequences.</param>
/// <returns>True if Parsed sequence properly.</returns>
private static bool TryParseSequenceFile(string fileName, IAlphabet alphabet, out IList <ISequence> sequences)
{
using (TextReader reader = new StreamReader(fileName))
{
string firstLine = reader.ReadLine();
if (ValidateFastaFormat(firstLine))
{
using (FastAParser parse = new FastAParser())
{
parse.Alphabet = alphabet;
sequences = parse.Parse().ToList();
}
return(true);
}
else if (ValidatePhylipFormat(firstLine))
{
PhylipParser parse = new PhylipParser();
parse.Alphabet = alphabet;
sequences = ConvertAlignedSequenceToSequence(parse.Parse(fileName));
return(true);
}
else if (ValidateTabFormat(firstLine))
{
using (FieldTextFileParser parse = new FieldTextFileParser(fileName))
{
parse.Alphabet = alphabet;
sequences = parse.Parse().ToList();
return(true);
}
}
else
{
sequences = null;
return(false);
}
}
}
