public void ProduceResult(IDataPoints data, ISpectrum spectrum, IGlycoPeptide glycoPeptide)
{
ITableNGlycan glycan = glycoPeptide.GetGlycan() as ITableNGlycan;
Dictionary <string, IPeak> peaks = new Dictionary <string, IPeak>();
List <IAnnotatedPeak> annotatedPeaks = new List <IAnnotatedPeak>();
foreach (PeakPoint pt in data.GetPoints())
{
if (!peaks.ContainsKey(pt.GetID()))
{
double mass = Double.Parse(pt.GetID());
peaks[pt.GetID()] = new GeneralPeak(mass, pt.GetIntensity());
}
List <IGlycoPeptide> glycoPeptides = new List <IGlycoPeptide>();
foreach (NGlycoPeptideNode node in pt.GetMaxNode())
{
if (IsGlycanMatch(node.GetNGlycan(), glycan))
{
glycoPeptides.Add(new GeneralGlycoPeptide(node.GetPeptide(), node.GetNGlycan(), -1));
}
}
if (glycoPeptides.Count > 0)
{
IAnnotatedPeak p = new GeneralAnnotatedSpectrumPeak(peaks[pt.GetID()], glycoPeptides);
annotatedPeaks.Add(p);
}
}
result = new GeneralAnnotatedSpectrumPeakResultProduct(spectrum,
annotatedPeaks.OrderBy(x => x.GetMZ()).ToList());
}
public void Annotate(ISpectrum spectrum, IGlycoPeptide glycoPeptide)
{
List <INode> roots = InitRoot(glycoPeptide);
IDataPoints data = InitSpectrum(spectrum);
dp.Search(roots, data, parameter as DPSpectrumCIDParameter);
ProduceResult(data, spectrum, glycoPeptide);
}
public void Annotate(ISpectrum spectrum, IGlycoPeptide glycoPeptide)
{
InitMatcher(glycoPeptide);
List <IAnnotatedPeak> peaks = GenerateMatcherResult(spectrum);
result = new GeneralAnnotatedSpectrumPeakResultProduct(spectrum, peaks);
}
public VectorScore(IGlycoPeptide glycoPeptide, double alpha, double beta,
Dictionary <MassType, double> weights)
{
this.glycoPeptide = glycoPeptide;
this.alpha = alpha;
this.beta = beta;
this.weights = weights;
peakSet = new HashSet <IPeak>();
matches = new Dictionary <MassType, List <IPeak> >();
}
protected List <INode> InitRoot(IGlycoPeptide glycoPeptide)
{
List <INode> rootList = new List <INode>();
foreach (ITableNGlycan g in CreateInitNGlycan.Creator.Create())
{
rootList.Add(new NGlycoPeptideNode(g, glycoPeptide.GetPeptide(), new PeakScore()));
}
return(rootList);
}
public List <IPoint> Create(IGlycoPeptide glycoPeptide, MassType type)
{
List <IPoint> points = new List <IPoint>();
foreach (double mass in (glycoPeptide as IGlycoPeptideMassProxy).GetMass(type))
{
points.Add(new GeneralPoint(mass));
}
return(points);
}
public WeightedScore(IGlycoPeptide glycoPeptide,
double alpha, double beta, Dictionary <MassType, double> weights)
{
this.glycoPeptide = glycoPeptide;
this.alpha = alpha;
this.beta = beta;
peakInclude = new HashSet <double>();
theory = new Dictionary <MassType, int>();
matches = new Dictionary <MassType, List <double> >();
this.weights = weights;
foreach (MassType type in weights.Keys)
{
theory[type] = (glycoPeptide as IGlycoPeptideMassProxy).GetMass(type).Count;
}
}
public void ReportLines(ISpectrum spectrum, List <IScore> scores)
{
HashSet <string> seen = new HashSet <string>();
Tuple <List <double[]>, double[]> predict = Predicting(scores);
int idx = 0;
foreach (IScore score in scores)
{
if (0 >= 0)
{
// get glycan
IGlycoPeptide glycoPeptide = score.GetGlycoPeptide();
// remove redudant
string structure = string.Join("_", glycoPeptide.GetGlycan().GetStructure());
string seq = glycoPeptide.GetPeptide().GetSequence();
if (!seen.Contains(structure + seq))
{
seen.Add(structure + seq);
}
else
{
continue;
}
writer.Write(spectrum.GetScanNum().ToString() + ", ");
writer.Write(seq + ", ");
writer.Write(structure + ", ");
writer.Write(score.GetScore(MassType.Core).ToString() + ", ");
writer.Write(score.GetScore(MassType.Branch).ToString() + ", ");
writer.Write(score.GetScore(MassType.Glycan).ToString() + ", ");
writer.Write(score.GetScore(MassType.Peptide).ToString() + ", ");
writer.Write((spectrum as ISpectrumMSn).GetParentMZ().ToString() + ", ");
writer.Write((spectrum as ISpectrumMSn).GetParentCharge().ToString() + ", ");
writer.Write(string.Join(".", predict.Item1[idx]) + ", ");
writer.Write(predict.Item2[idx].ToString() + ", ");
writer.WriteLine();
}
idx++;
}
}
public void ReportLines(List <IProbScoreProxy> scores, double cutoff)
{
HashSet <string> seen = new HashSet <string>();
int idx = 0;
foreach (IProbScoreProxy score in scores)
{
if (score.GetProbability() > cutoff)
{
// get glycan
IGlycoPeptide glycoPeptide = score.GetGlycoPeptide();
// remove redudant
string structure = string.Join("_", glycoPeptide.GetGlycan().GetStructure());
string seq = glycoPeptide.GetPeptide().GetSequence();
if (!seen.Contains(structure + seq))
{
seen.Add(structure + seq);
}
else
{
continue;
}
writer.Write(score.GetSpectrum().GetScanNum().ToString() + ", ");
writer.Write(seq + ", ");
writer.Write(structure + ", ");
writer.Write(score.GetScore(MassType.Core).ToString() + ", ");
writer.Write(score.GetScore(MassType.Branch).ToString() + ", ");
writer.Write(score.GetScore(MassType.Glycan).ToString() + ", ");
writer.Write(score.GetScore(MassType.Peptide).ToString() + ", ");
writer.Write((score.GetSpectrum() as ISpectrumMSn).GetParentMZ().ToString() + ", ");
writer.Write((score.GetSpectrum() as ISpectrumMSn).GetParentCharge().ToString() + ", ");
writer.Write(score.GetProbability().ToString() + ", ");
writer.Write(cutoff + ", ");
writer.Write(score.IsDecoy() + ", ");
writer.WriteLine();
}
idx++;
}
}
protected void ReportLines(ISpectrum spectrum, List <IScore> scores, double cutoff)
{
HashSet <string> seen = new HashSet <string>();
foreach (IScore score in scores)
{
if (score.GetScore() > cutoff)
{
// get glycan
IGlycoPeptide glycoPeptide = score.GetGlycoPeptide();
// remove redudant
string structure = string.Join("_", glycoPeptide.GetGlycan().GetStructure());
string seq = glycoPeptide.GetPeptide().GetSequence();
if (!seen.Contains(structure + seq))
{
seen.Add(structure + seq);
}
else
{
continue;
}
writer.Write(spectrum.GetScanNum().ToString() + ", ");
writer.Write(seq + ", ");
writer.Write(structure + ", ");
writer.Write(score.GetScore(MassType.Branch).ToString() + ", ");
writer.Write(score.GetScore(MassType.Core).ToString() + ", ");
writer.Write(score.GetScore(MassType.Glycan).ToString() + ", ");
writer.Write(score.GetScore(MassType.Peptide).ToString() + ", ");
writer.Write((spectrum as ISpectrumMSn).GetParentMZ().ToString() + ", ");
writer.Write((spectrum as ISpectrumMSn).GetParentCharge().ToString() + ", ");
if (score is IFDRScoreProxy)
{
writer.Write((score as IFDRScoreProxy).IsDecoy());
writer.Write(", ");
}
writer.WriteLine();
}
}
}
public IScore CreateScore(IGlycoPeptide glycoPeptide)
{
return(new VectorScore(glycoPeptide, alpha, beta, weights));
}
public GeneralGlycoPeptideMassProxy(IGlycoPeptide glycoPeptide) : base(glycoPeptide)
{
massTable = new Dictionary <MassType, HashSet <double> >();
}
public GeneralGlycoPeptideScore(IGlycoPeptide glycoPeptide, double score) :
base(glycoPeptide.GetPeptide(), glycoPeptide.GetGlycan(), glycoPeptide.GetPosition())
{
this.glycoPeptide = glycoPeptide;
this.score = score;
}
public GlycoPeptideProxyTemplate(IGlycoPeptide glycoPeptide)
{
this.glycoPeptide = glycoPeptide;
}
protected void InitMatcher(IGlycoPeptide glycoPeptide)
{
List <Point> points = new List <Point>();
List <ITableNGlycan> glycans = glycansTable[
glycoPeptide.GetGlycan().GetName()];
IPeptide peptide = glycoPeptide.GetPeptide();
string seq = peptide.GetSequence();
int pos = glycoPeptide.GetPosition();
Dictionary <double, BinSearchAnnotatedPoint> seen =
new Dictionary <double, BinSearchAnnotatedPoint>();
//glycanfrag
foreach (ITableNGlycan g in glycans)
{
double glycanMass = calculator.CalcGlycanMass(g, option);
double mass = calculator.CalcPeptideMass(seq, option) + glycanMass;
if (!seen.ContainsKey(mass))
{
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
seen[mass] = p;
points.Add(p);
}
seen[mass].AddGlycoPeptide(
new GeneralPeptide(peptide.GetID(), seq), g, pos);
//n-peptidefrag
for (int i = 0; i < pos; i++)
{
mass = calculator.CalcPeptideIonMass(
seq.Substring(0, i + 1), IonType.cIon, option) + glycanMass;
if (!seen.ContainsKey(mass))
{
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
seen[mass] = p;
points.Add(p);
}
seen[mass].AddGlycoPeptide(
new GeneralPeptide(peptide.GetID(), seq.Substring(0, i + 1)),
g, pos);
}
//c-peptidefrag
for (int i = pos + 1; i < seq.Length; i++)
{
mass = calculator.CalcPeptideIonMass(
seq.Substring(i, seq.Length - i), IonType.zIon, option) + glycanMass;
if (!seen.ContainsKey(mass))
{
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
seen[mass] = p;
points.Add(p);
}
seen[mass].AddGlycoPeptide(
new GeneralPeptide(peptide.GetID(), seq.Substring(i, seq.Length - i)),
g, pos);
}
}
points.Sort();
matcher.SetPoints(points);
}
public void AddFragment(IGlycoPeptide glycoPeptide)
{
glycoPeptides.Add(glycoPeptide);
}
