public static int[] GetSequenceCoverage(this AminoAcidPolymer baseSequence, IEnumerable <AminoAcidPolymer> allPolymers, bool useLeucineSequence)
{
int[] bits = new int[baseSequence.Length];
string masterSequence = useLeucineSequence ? baseSequence.BaseLeucineSequence : baseSequence.BaseSequence;
foreach (AminoAcidPolymer polymer in allPolymers)
{
string seq = useLeucineSequence ? polymer.BaseLeucineSequence : polymer.BaseSequence;
int startIndex = 0;
while (true)
{
int index = masterSequence.IndexOf(seq, startIndex, StringComparison.Ordinal);
if (index < 0)
{
break;
}
for (int aa = index; aa < index + polymer.Length; aa++)
{
bits[aa]++;
}
startIndex = index + 1;
}
}
return(bits);
}
/// <summary>
/// Create a new peptide based on another amino acid polymer
/// </summary>
/// <param name="aminoAcidPolymer">The other amino acid polymer to copy</param>
/// <param name="includeModifications">Whether to copy the modifications to the new peptide</param>
public Peptide(AminoAcidPolymer aminoAcidPolymer, bool includeModifications)
: base(aminoAcidPolymer, includeModifications)
{
Parent = aminoAcidPolymer;
StartResidue = 0;
EndResidue = Length - 1;
}
public Fragment(FragmentTypes type, int number, double monoisotopicMass, AminoAcidPolymer parent)
{
FragmentType = type;
Number = number;
Parent = parent;
MonoisotopicMass = monoisotopicMass;
}
public Peptide(AminoAcidPolymer aminoAcidPolymer, int firstResidue, int length, bool includeModifications)
: base(aminoAcidPolymer, firstResidue, length, includeModifications)
{
Parent = aminoAcidPolymer;
StartResidue = firstResidue;
EndResidue = firstResidue + length - 1;
PreviousResidue = aminoAcidPolymer.GetResidue(StartResidue - 1);
NextResidue = aminoAcidPolymer.GetResidue(EndResidue + 1);
}
public ChemicalFormulaFragment(FragmentTypes type, int number, ChemicalFormula formula, AminoAcidPolymer parent)
: base(type, number, formula.MonoisotopicMass, parent)
{
ThisChemicalFormula = ChemicalFormula.ParseFormula(formula.Formula);
}
public Peptide(AminoAcidPolymer aminoAcidPolymer, int firstResidue, int length)
: this(aminoAcidPolymer, firstResidue, length, true)
{
}
public Peptide(AminoAcidPolymer aminoAcidPolymer)
: this(aminoAcidPolymer, true)
{
}
public static int[] GetSequenceCoverage(this AminoAcidPolymer baseSequence, IEnumerable <AminoAcidPolymer> sequences)
{
return(GetSequenceCoverage(baseSequence, sequences, true));
}
public static double GetSequenceCoverageFraction(this AminoAcidPolymer baseSequence, IEnumerable <AminoAcidPolymer> sequences, bool useLeucineSequence)
{
int[] counts = baseSequence.GetSequenceCoverage(sequences, useLeucineSequence);
return(((double)counts.Count(x => x > 0)) / baseSequence.Length);
}
public static double GetSequenceCoverageFraction(this AminoAcidPolymer baseSequence, IEnumerable <AminoAcidPolymer> sequences)
{
return(GetSequenceCoverageFraction(baseSequence, sequences, true));
}
