public static bool TryGetMatrixFromSequenceFileAndPossiblyConvertDna2Aa <TRow, TCol, TVal>(string filename, TVal missing, bool keepOneValueVariables, ParallelOptions parallelOptions, out Matrix <TRow, TCol, TVal> matrix)
{
SequenceFormatter formatter;
matrix = null;
if (SequenceFormatter.TryGetLikelyFormatterForFile(filename, out formatter))
{
// only support true sequence formats.
if (formatter is SequenceMatrix)
{
return(false);
}
var seqs = formatter.Parse(filename);
if (seqs.Count == 0)
{
return(false);
}
if (seqs[0].IsDna())
{
seqs = Translate(seqs, true);
}
matrix = NamedSequencesToMatrix <TRow, TCol, TVal>(seqs, missing, keepOneValueVariables, parallelOptions);
return(true);
}
return(false);
}
public static bool TryGetMatrixFromSequenceFile <TRow, TCol, TVal>(string filename, TVal missing, bool keepOneValueVariables, ParallelOptions parallelOptions, out Matrix <TRow, TCol, TVal> matrix)
{
SequenceFormatter formatter;
matrix = null;
if (SequenceFormatter.TryGetLikelyFormatterForFile(filename, out formatter))
{
// only support true sequence formats.
if (formatter is SequenceMatrix)// || formatter is SequenceFormatterSparse)
{
return(false);
}
var seqs = formatter.Parse(filename);
if (seqs.Count == 0)
{
Console.Error.WriteLine("No sequences in sequence file of format {0}", formatter.FileFormat);
return(false);
}
matrix = NamedSequencesToMatrix <TRow, TCol, TVal>(seqs, missing, keepOneValueVariables, parallelOptions);
return(true);
//if (IsDna(seqs[0].Sequence))
//{
// seqs = NucSeqToAaSeq(seqs, true);
//}
}
Console.Error.WriteLine("No SequenceFormatter matches this file type.");
return(false);
}