public override SortedMaxSizedContainer <PeptideSpectralMatch> Search(IMassSpectrum spectrum, IEnumerable <Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer <PeptideSpectralMatch> results = new SortedMaxSizedContainer <PeptideSpectralMatch>(MaxMatchesPerSpectrum);
double[] eMasses = spectrum.MassSpectrum.GetMasses();
double[] eIntenisties = spectrum.MassSpectrum.GetIntensities();
double tic = spectrum.MassSpectrum.GetTotalIonCurrent();
;
foreach (var peptide in peptides)
{
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType)
{
Peptide = peptide
};
double[] tMasses =
peptide.Fragment(fragmentTypes)
.Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1))
.OrderBy(val => val)
.ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
results.Add(psm);
}
return(results);
}
public virtual SortedMaxSizedContainer <PeptideSpectralMatch> Search(IMassSpectrum massSpectrum, IEnumerable <Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer <PeptideSpectralMatch> results = new SortedMaxSizedContainer <PeptideSpectralMatch>(MaxMatchesPerSpectrum);
foreach (var peptide in peptides)
{
results.Add(Search(massSpectrum, peptide, fragmentTypes, productMassTolerance));
}
return(results);
}
public override PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
double[] eMasses = massSpectrum.MassSpectrum.GetMasses();
double[] eIntenisties = massSpectrum.MassSpectrum.GetIntensities();
double tic = massSpectrum.MassSpectrum.GetTotalIonCurrent();
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType) {Peptide = peptide};
double[] tMasses = peptide.Fragment(fragmentTypes).Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1)).OrderBy(val => val).ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
return psm;
}
public override PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
double[] eMasses = massSpectrum.MassSpectrum.GetMasses();
double[] eIntenisties = massSpectrum.MassSpectrum.GetIntensities();
double tic = massSpectrum.MassSpectrum.GetTotalIonCurrent();
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType)
{
Peptide = peptide
};
double[] tMasses = peptide.Fragment(fragmentTypes).Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1)).OrderBy(val => val).ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
return(psm);
}
public override SortedMaxSizedContainer<PeptideSpectralMatch> Search(IMassSpectrum spectrum, IEnumerable<Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer<PeptideSpectralMatch> results = new SortedMaxSizedContainer<PeptideSpectralMatch>(MaxMatchesPerSpectrum);
double[] eMasses = spectrum.MassSpectrum.GetMasses();
double[] eIntenisties = spectrum.MassSpectrum.GetIntensities();
double tic = spectrum.MassSpectrum.TotalIonCurrent;
foreach (var peptide in peptides)
{
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType) {Peptide = peptide};
double[] tMasses =
peptide.Fragment(fragmentTypes)
.Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1))
.OrderBy(val => val)
.ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
results.Add(psm);
}
return results;
}
public virtual SortedMaxSizedContainer<PeptideSpectralMatch> Search(IMassSpectrum massSpectrum, IEnumerable<Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer<PeptideSpectralMatch> results = new SortedMaxSizedContainer<PeptideSpectralMatch>(MaxMatchesPerSpectrum);
foreach (var peptide in peptides)
{
results.Add(Search(massSpectrum, peptide, fragmentTypes, productMassTolerance));
}
return results;
}
public virtual SortedMaxSizedContainer<PeptideSpectralMatch> Search(IMassSpectrum massSpectrum, IEnumerable<Peptide> peptides)
{
return Search(massSpectrum, peptides, DefaultFragmentType, ProductMassTolerance);
}
public abstract PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance);
public virtual PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide)
{
return Search(massSpectrum, peptide, DefaultFragmentType, ProductMassTolerance);
}
public virtual SortedMaxSizedContainer <PeptideSpectralMatch> Search(IMassSpectrum massSpectrum, IEnumerable <Peptide> peptides)
{
return(Search(massSpectrum, peptides, DefaultFragmentType, ProductMassTolerance));
}
public abstract PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance);
public virtual PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide)
{
return(Search(massSpectrum, peptide, DefaultFragmentType, ProductMassTolerance));
}
