/// <summary>
/// Given a protein sequence, a collection of peptides will be returned.
/// Assumes conventional trypsin digest and max 1 missed cleavage.
/// </summary>
/// <param name="proteinSequence">The protein sequence to digest.</param>
/// <param name="digestionRule">Determines which digestion rule to use (fully tryptic, partially tryptic, no rules).</param>
/// <param name="maxMissedCleavages">The maximum number of missed cleavages to consider.</param>
/// <returns>An IEnumerable of Peptide objects.</returns>
public static IEnumerable<clsInSilicoDigest.PeptideInfoClass> DigestProtein(string proteinSequence, clsInSilicoDigest.CleavageRuleConstants digestionRule, int maxMissedCleavages)
{
clsParseProteinFile parseProteinFile = new clsParseProteinFile
{
AssumeFastaFile = true,
AssumeDelimitedFile = false,
ComputeProteinMass = true,
CreateProteinOutputFile = false,
CreateDigestedProteinOutputFile = false,
GenerateUniqueIDValuesForPeptides = true
};
clsInSilicoDigest.PeptideInfoClass[] peptideArray = new clsInSilicoDigest.PeptideInfoClass[1];
clsInSilicoDigest.DigestionOptionsClass digestionOptions = new clsInSilicoDigest.DigestionOptionsClass
{
CleavageRuleID = digestionRule,
MaxMissedCleavages = maxMissedCleavages
};
parseProteinFile.DigestProteinSequence(proteinSequence, ref peptideArray, digestionOptions, "xlinkProt");
return peptideArray;
}
/// <summary>
/// Given a protein sequence, a collection of peptides will be returned.
/// Assumes conventional trypsin digest and max 1 missed cleavage.
/// </summary>
/// <param name="proteinSequence">The protein sequence to digest.</param>
/// <param name="digestionRule">Determines which digestion rule to use (fully tryptic, partially tryptic, no rules).</param>
/// <param name="maxMissedCleavages">The maximum number of missed cleavages to consider.</param>
/// <returns>An IEnumerable of Peptide objects.</returns>
public static IEnumerable <clsInSilicoDigest.PeptideInfoClass> DigestProtein(string proteinSequence, clsInSilicoDigest.CleavageRuleConstants digestionRule, int maxMissedCleavages)
{
clsParseProteinFile parseProteinFile = new clsParseProteinFile
{
AssumeFastaFile = true,
AssumeDelimitedFile = false,
ComputeProteinMass = true,
CreateProteinOutputFile = false,
CreateDigestedProteinOutputFile = false,
GenerateUniqueIDValuesForPeptides = true
};
clsInSilicoDigest.PeptideInfoClass[] peptideArray = new clsInSilicoDigest.PeptideInfoClass[1];
clsInSilicoDigest.DigestionOptionsClass digestionOptions = new clsInSilicoDigest.DigestionOptionsClass
{
CleavageRuleID = digestionRule,
MaxMissedCleavages = maxMissedCleavages
};
parseProteinFile.DigestProteinSequence(proteinSequence, ref peptideArray, digestionOptions, "xlinkProt");
return(peptideArray);
}