/// <summary>
/// Creates a PeptideWithSetModifications object from a sequence string.
/// Useful for reading in MetaMorpheus search engine output into mzLib objects.
/// </summary>
public PeptideWithSetModifications(string sequence, Dictionary <string, Modification> allKnownMods, int numFixedMods = 0,
DigestionParams digestionParams = null, Protein p = null, int oneBasedStartResidueInProtein = int.MinValue,
int oneBasedEndResidueInProtein = int.MinValue, int missedCleavages = int.MinValue,
CleavageSpecificity cleavageSpecificity = CleavageSpecificity.Full, string peptideDescription = null)
: base(p, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein, missedCleavages, cleavageSpecificity, peptideDescription)
{
if (sequence.Contains("|"))
{
throw new MzLibUtil.MzLibException("Ambiguous peptide cannot be parsed from string: " + sequence);
}
FullSequence = sequence;
GetModsAfterDeserialization(allKnownMods, out _baseSequence);
NumFixedMods = numFixedMods;
_digestionParams = digestionParams;
if (p != null)
{
ProteinAccession = p.Accession;
}
if (digestionParams != null)
{
DigestionParamString = digestionParams.ToString();
}
}
private readonly string ProteinAccession; // used to get protein object after deserialization
/// <summary>
/// Creates a PeptideWithSetModifications object from a protein. Used when a Protein is digested.
/// </summary>
public PeptideWithSetModifications(Protein protein, DigestionParams digestionParams, int oneBasedStartResidueInProtein,
int oneBasedEndResidueInProtein, string peptideDescription, int missedCleavages,
Dictionary <int, Modification> allModsOneIsNterminus, int numFixedMods)
: base(protein, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein, missedCleavages, peptideDescription)
{
_allModsOneIsNterminus = allModsOneIsNterminus;
NumFixedMods = numFixedMods;
_digestionParams = digestionParams;
DetermineFullSequence();
ProteinAccession = protein.Accession;
DigestionParamString = digestionParams.ToString();
}