public override bool Equals(object obj)
{
if (this == obj)
{
return(true);
}
if (obj is AminoAcid)
{
AminoAcid other = (AminoAcid)obj;
return(other.letter == letter);
}
return(false);
}
public LabelCombinations(SilacLabel[] labelsLow, SilacLabel[] labelsHigh, int maxNum, char[] allAaLetts)
{
AminoAcid[] aasHigh = new AminoAcid[labelsHigh.Length];
char[] aaLettsHigh = new char[labelsHigh.Length];
Molecule[] labelingDiff1High = new Molecule[labelsHigh.Length];
Molecule[] labelingDiff2High = new Molecule[labelsHigh.Length];
for (int i = 0; i < labelsHigh.Length; i++)
{
aasHigh[i] = AminoAcid.GetAminoAcidFromLabel(labelsHigh[i]);
aaLettsHigh[i] = aasHigh[i].Letter;
labelingDiff1High[i] = aasHigh[i].GetLabelingDiff1(labelsHigh[i]);
labelingDiff2High[i] = aasHigh[i].GetLabelingDiff2(labelsHigh[i]);
}
AminoAcid[] aasLow = new AminoAcid[labelsLow.Length];
char[] aaLettsLow = new char[labelsLow.Length];
Molecule[] labelingDiff1Low = new Molecule[labelsLow.Length];
Molecule[] labelingDiff2Low = new Molecule[labelsLow.Length];
for (int i = 0; i < labelsLow.Length; i++)
{
aasLow[i] = AminoAcid.GetAminoAcidFromLabel(labelsLow[i]);
aaLettsLow[i] = aasLow[i].Letter;
labelingDiff1Low[i] = aasLow[i].GetLabelingDiff1(labelsLow[i]);
labelingDiff2Low[i] = aasLow[i].GetLabelingDiff2(labelsLow[i]);
}
int[] indLow = new int[allAaLetts.Length];
int[] indHigh = new int[allAaLetts.Length];
for (int i = 0; i < allAaLetts.Length; i++)
{
indLow[i] = ArrayUtil.IndexOf(aaLettsLow, allAaLetts[i]);
indHigh[i] = ArrayUtil.IndexOf(aaLettsHigh, allAaLetts[i]);
}
labelingDiff1 = new Molecule[allAaLetts.Length];
labelingDiff2 = new Molecule[allAaLetts.Length];
for (int i = 0; i < allAaLetts.Length; i++)
{
if (indLow[i] >= 0 && indHigh[i] >= 0)
{
labelingDiff1[i] = Molecule.Sum(labelingDiff2Low[indLow[i]], labelingDiff1High[indHigh[i]]);
labelingDiff2[i] = Molecule.Sum(labelingDiff1Low[indLow[i]], labelingDiff2High[indHigh[i]]);
Molecule[] w = Molecule.GetDifferences(labelingDiff1[i], labelingDiff2[i]);
labelingDiff1[i] = w[0];
labelingDiff2[i] = w[1];
}
else if (indLow[i] >= 0 && indHigh[i] < 0)
{
labelingDiff1[i] = labelingDiff2Low[indLow[i]];
labelingDiff2[i] = labelingDiff1Low[indLow[i]];
}
else if (indLow[i] < 0 && indHigh[i] >= 0)
{
labelingDiff1[i] = labelingDiff1High[indHigh[i]];
labelingDiff2[i] = labelingDiff2High[indHigh[i]];
}
else
{
throw new Exception("Should not happen.");
}
}
partitions = GetPartitions(maxNum, allAaLetts.Length);
isotopeDistr1 = new double[partitions.Length][][];
isotopeDistr2 = new double[partitions.Length][][];
for (int i = 0; i < partitions.Length; i++)
{
isotopeDistr1[i] = CalcDiff1(partitions[i]).GetIsotopeDistribution(0.2);
isotopeDistr2[i] = CalcDiff2(partitions[i]).GetIsotopeDistribution(0.2);
}
maxMassDiff = 0;
for (int i = 0; i < allAaLetts.Length; i++)
{
double diff = Math.Abs(labelingDiff1[i].GetMostLikelyMass(0.2) -
labelingDiff2[i].GetMostLikelyMass(0.2));
if (diff > maxMassDiff)
{
maxMassDiff = diff;
}
}
maxMassDiff *= maxNum;
}
