/// <summary>
/// Score a <see cref="PrSm" /> based on its sequence and MS/MS spectrum.
/// </summary>
/// <param name="prsm">The <see cref="PrSm" /> to score.</param>
private void UpdatePrSmScore(PrSm prsm)
{
if (this.ScorerFactory == null)
{
return;
}
var ms2Spectrum = prsm.Ms2Spectrum;
if (ms2Spectrum == null)
{
return;
}
var scorer = this.ScorerFactory.GetScorer(prsm.Ms2Spectrum);
prsm.Score = IonUtils.ScoreSequence(scorer, prsm.Sequence);
}
/// <summary>
/// Implementation of the CreatePRSM command.
/// Creates a new protein-spectrum match for the selected sequence,
/// charge, and scan number.
/// </summary>
private void CreatePrSmImplementation()
{
var sequenceReader = new SequenceReader();
Sequence sequence = null;
try
{
sequence = sequenceReader.Read(this.SequenceText);
if (sequence == null)
{
throw new FormatException("Invalid Sequence.");
}
}
catch (FormatException e)
{
this.dialogService.MessageBox(e.Message);
return;
}
finally
{
if (sequence == null)
{
sequence = new Sequence(new List <AminoAcid>());
}
}
if (sequence.Count > 0 && this.SelectedCharge == 0)
{
this.dialogService.MessageBox("Invalid Charge state.");
return;
}
if (sequence.Count == 0 && this.SelectedScan < 0)
{
this.dialogService.MessageBox("Invalid scan number.");
return;
}
ILcMsRun lcms = this.SelectedDataSetViewModel.LcMs;
double score = -1.0;
if (lcms != null && this.SelectedScan > 0 && this.ScorerFactory != null && sequence.Count > 0)
{
var spectrum = lcms.GetSpectrum(this.SelectedScan) as ProductSpectrum;
if (spectrum != null)
{
var scorer = this.ScorerFactory.GetScorer(spectrum);
score = IonUtils.ScoreSequence(scorer, sequence);
}
}
string rawFileName = this.SelectedDataSetViewModel.Title;
var prsm = new PrSm
{
Heavy = false,
RawFileName = rawFileName,
ProteinName = string.Empty,
ProteinDesc = string.Empty,
Scan = Math.Min(Math.Max(this.SelectedScan, 0), lcms.MaxLcScan),
LcMs = lcms,
Charge = this.SelectedCharge,
Sequence = sequence,
SequenceText = this.SequenceText,
Score = score,
};
this.SelectedPrSm = prsm;
}
