public int GetNumberOfTheoreticalPeptides(Protease protease, int minLength, int maxLength)
{
if (!theoreticalPeptides.ContainsKey(protease))
{
CalculateTheoreticalPeptides(protease, minLength, maxLength, 0, double.PositiveInfinity);
}
return(theoreticalPeptides[protease].Length);
}
public PeptideSequence[] GetTheoreticalPeptides(Protease protease)
{
if (!theoreticalPeptides.ContainsKey(protease))
{
CalculateTheoreticalPeptides(protease);
}
return(theoreticalPeptides[protease]);
}
public int GetNumberOfTheoreticalPeptides(Protease protease)
{
if (!theoreticalPeptides.ContainsKey(protease))
{
CalculateTheoreticalPeptides(protease);
}
return(theoreticalPeptides[protease].Length);
}
public PeptideSequence[] GetTheoreticalPeptides(Protease protease, int minLength, int maxLength)
{
if (!theoreticalPeptides.ContainsKey(protease))
{
CalculateTheoreticalPeptides(protease, minLength, maxLength, 0, double.PositiveInfinity);
}
return(theoreticalPeptides[protease]);
}
private void CalculateTheoreticalPeptides(Protease protease)
{
int minLength = 7;
int maxLength = 30;
double minWeight = 0;
double maxWeight = double.PositiveInfinity;
CalculateTheoreticalPeptides(protease, minLength, maxLength, minWeight, maxWeight);
}
public int GetNumberOfTheoreticalPeptides()
{
Protease protease = Constants.trypsin;
if (!theoreticalPeptides.ContainsKey(protease))
{
CalculateTheoreticalPeptides(protease);
}
return(theoreticalPeptides[protease].Length);
}
public PeptideSequence[] GetTheoreticalPeptides()
{
Protease protease = Constants.trypsin;
if (!theoreticalPeptides.ContainsKey(protease))
{
CalculateTheoreticalPeptides(protease);
}
return(theoreticalPeptides[protease]);
}
public string[] GetTheoreticalPeptideSequences(Protease protease, int minLength, int maxLength)
{
PeptideSequence[] peptides = GetTheoreticalPeptides(protease, minLength, maxLength);
List <string> peptideSequences = new List <string>();
foreach (PeptideSequence peptide in peptides)
{
peptideSequences.Add(peptide.GetSequence());
}
return(peptideSequences.ToArray());
}
// generic method; protease and margins can be defined
private void CalculateTheoreticalPeptides(Protease protease, int minLength, int maxLength, double minWeight,
double maxWeight)
{
MatchCollection peptideMatches = protease.cleavageSpecificity.Matches(GetSequence());
List <PeptideSequence> theoreticalPeptides1 = new List <PeptideSequence>();
foreach (Match match in peptideMatches)
{
PeptideSequence theoreticalPeptide = new PeptideSequence();
theoreticalPeptide.SetSequence(match.Groups[1].Value);
if (theoreticalPeptide.GetLength() >= minLength && theoreticalPeptide.GetLength() <= maxLength &&
(minWeight > 0 && maxWeight < double.PositiveInfinity // speed up calculations in case there are no weight limits
||
theoreticalPeptide.GetMonoisotopicMolecularMass() >= minWeight &&
theoreticalPeptide.GetMonoisotopicMolecularMass() <= maxWeight))
{
theoreticalPeptides1.Add(theoreticalPeptide);
}
}
theoreticalPeptides[protease] = theoreticalPeptides1.ToArray();
}
