/// <summary>
/// Parse a CLEAN sequence (containing no pre/post residues or modifications).
/// </summary>
/// <param name="sequenceText">The clean sequence.</param>
/// <param name="modInfo">The modification info for the sequence.</param>
/// <returns>The parsed sequence.</returns>
private Sequence ParseSequence(string sequenceText, List <clsAminoAcidModInfo> modInfo)
{
var sequenceReader = new SequenceReader();
var sequence = sequenceReader.Read(sequenceText);
foreach (var mod in modInfo)
{
if (mod.AmbiguousMod)
{
continue;
}
var location = mod.ResidueLocInPeptide - 1;
var aminoAcid = sequence[location];
var modification = TryGetExistingModification(
mod.ModDefinition.MassCorrectionTag,
mod.ModDefinition.ModificationMass);
if (modification == null)
{ // could not find existing modification
modification = new Modification(0, mod.ModDefinition.ModificationMass, mod.ModDefinition.MassCorrectionTag);
Modifications.Add(modification);
}
sequence[location] = new ModifiedAminoAcid(aminoAcid, modification);
}
// Force it to recalculate mass now that the modifications have been added.
sequence = new Sequence(sequence);
return(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;
}