public static Matrix <TRow, TCol, TVal> NamedSequencesToMatrix <TRow, TCol, TVal>(List <NamedSequence> seqs, TVal missing, bool keepOneValueVariables, ParallelOptions parallelOptions)
{
Helper.CheckCondition(seqs.Count > 0, "There are no sequences");
// can't do this because of the generics
//var matrix = SequenceMatrix.ConvertToMatrix(seqs, MixtureSemantics.Uncertainty, SequenceMatrix.BinaryOrMultistate.Binary, keepOneValueVariables);
string tempFile = Path.GetTempFileName();
SequenceMatrix tableFormatter = new SequenceMatrix();
tableFormatter.KeepOneValueVariables = keepOneValueVariables;
////if (keepOneValueVariables)
////{
//// tableFormatter.argumentCollection = new CommandArguments("-keepOneValueVariables");
////}
tableFormatter.Write(seqs, tempFile);
Matrix <TRow, TCol, TVal> matrix;
bool success = DenseMatrix <TRow, TCol, TVal> .TryParseRFileWithDefaultMissing(tempFile, missing, parallelOptions, out matrix);
File.Delete(tempFile);
if (!success)
{
throw new Exception("Unexpected error parsing the table into a matrix. This exception should not happen.");
}
return(matrix);
}
public static SequenceFormatter GetInstance(SequenceFileFormat format)
{
SequenceFormatter formatter = null;
switch (format)
{
case SequenceFileFormat.Phylip:
formatter = new Phylip();
break;
case SequenceFileFormat.Fasta:
formatter = new Fasta();
break;
case SequenceFileFormat.Tab:
formatter = new Tab();
break;
//case SequenceFileFormat.Sparse:
// formatter = new SequenceFormatterSparse();
// break;
case SequenceFileFormat.Matrix:
formatter = new SequenceMatrix();
break;
default:
throw new Exception("Should never get here.");
}
formatter._formatType = format;
return(formatter);
}