public PeptideResultSpectraInputReader(
IPeptideResultReader peptideReader,
ISpectraReader spectralReader,
PhosphoRSOptions options = null
)
{
if (peptideReader == null)
{
throw new ArgumentNullException(nameof(peptideReader));
}
if (spectralReader == null)
{
throw new ArgumentNullException(nameof(spectralReader));
}
_peptideReader = peptideReader;
_spectralReader = spectralReader;
_options = options;
}
private IPhosphoRSInputReader GetInputReader(string peptide, string spectra, PhosphoRSOptions options = null)
{
IO.PeptideResult.IPeptideResultReader peptideReader;
{
var ext = System.IO.Path.GetExtension(peptide);
if (ext.Equals(".xml", StringComparison.InvariantCultureIgnoreCase))
{
peptideReader = new IO.PeptideResult.PepXmlReader(peptide);
}
else if (ext.Equals(".pepXML", StringComparison.InvariantCultureIgnoreCase))
{
peptideReader = new IO.PeptideResult.PepXmlReader(peptide);
}
else
{
peptideReader = new IO.PeptideResult.PepXmlReader(peptide);
}
}
IO.Spectral.ISpectraReader spectraReader;
{
var ext = System.IO.Path.GetExtension(spectra);
if (ext.Equals(".mgf", StringComparison.InvariantCultureIgnoreCase))
{
spectraReader = new IO.Spectral.MgfReader(spectra);
}
else if (ext.Equals(".mzXML", StringComparison.InvariantCultureIgnoreCase))
{
throw new NotImplementedException(".mzXML");
}
else
{
spectraReader = new IO.Spectral.MgfReader(spectra);
}
}
return(new IO.PeptideResultSpectraInputReader(peptideReader, spectraReader, options));
}
