/*
* Returns the protein accessions which are uniquely found in this class (and
* not found in the passed in protein prophet file).
*/
public List <String> compareProteins(ProteinProphetFile ppf)
{
List <String> uniqueProteins = new List <String>();
foreach (String proteinAccession in proteinsToPeptides.Keys)
{
bool notFoundInOtherPPF = ppf.containsProtein(proteinAccession);
if (notFoundInOtherPPF)
{
uniqueProteins.Add(proteinAccession);
}
}
return(uniqueProteins);
}
/*
* Returns the set of peptides (mapping to a protein accession) found in this
* protein prophet file but not in the other.
*/
public Dictionary <String, List <String> > comparePeptides(ProteinProphetFile ppf)
{
Dictionary <String, List <String> > uniqueProteinToPeptides = new Dictionary <String, List <String> >();
foreach (String proteinAccession in proteinsToPeptides.Keys)
{
List <String> peptides = proteinsToPeptides[proteinAccession];
List <String> uniquePeptides = new List <String>();
foreach (String peptideSequence in peptides)
{
bool notFoundInOtherPPF = ppf.containsPeptide(proteinAccession, peptideSequence);
if (notFoundInOtherPPF)
{
uniquePeptides.Add(peptideSequence);
}
}
if (uniquePeptides.Count != 0)
{
uniqueProteinToPeptides.Add(proteinAccession, uniquePeptides);
}
}
return(uniqueProteinToPeptides);
}