public SpectraPredictor(SpectralPredictionParameters myparams)
{
myParams = myparams;
aam = new AminoacidMasses();
if (myParams.IsMonoisotopic)
{
aaDict = PatternTools.ObjectCopier.Clone(aam.IsotopicDic);
}
else
{
aaDict = PatternTools.ObjectCopier.Clone(aam.AverageDic);
}
//Handle the modifications
foreach (ModificationItem m in myparams.MyModifications)
{
if (m.IsVariable)
{
string key = m.AminoAcid + "(" + m.DeltaMass + ")";
double mass = m.DeltaMass + aaDict[m.AminoAcid];
aaDict.Add(key, mass);
}
else
{
aaDict[m.AminoAcid] += m.DeltaMass;
}
}
}
public SequentialScore(double ppmTolerance, List <ModificationItem> modifications, double intensityPercentageCuttoff, int resultBuffer)
{
PatternTools.AminoacidMasses aa = new AminoacidMasses();
gapItems = aa.GenerateDeltaMassTable2(ppmTolerance, modifications);
largestGap = gapItems.Max(a => a.GapSize) + 0.3;
this.ppmTolerance = ppmTolerance;
this.intensityPercentageCuttoff = intensityPercentageCuttoff;
this.resultBuffer = resultBuffer;
}