/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="ph"></param>
/// <param name="idata"></param>
public PeptideHypothesisObj(PeptideHypothesisType ph, IdentDataObj idata)
: base(idata)
{
PeptideEvidenceRef = ph.peptideEvidence_ref;
SpectrumIdentificationItems = new IdentDataList <SpectrumIdentificationItemRefObj>(1);
if (ph.SpectrumIdentificationItemRef?.Count > 0)
{
SpectrumIdentificationItems.AddRange(ph.SpectrumIdentificationItemRef, spectrumIdItemRef => new SpectrumIdentificationItemRefObj(spectrumIdItemRef, IdentData));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="ph"></param>
/// <param name="idata"></param>
public PeptideHypothesisObj(PeptideHypothesisType ph, IdentDataObj idata)
: base(idata)
{
PeptideEvidenceRef = ph.peptideEvidence_ref;
_spectrumIdentificationItems = null;
if (ph.SpectrumIdentificationItemRef != null && ph.SpectrumIdentificationItemRef.Count > 0)
{
SpectrumIdentificationItems = new IdentDataList <SpectrumIdentificationItemRefObj>();
foreach (var siir in ph.SpectrumIdentificationItemRef)
{
SpectrumIdentificationItems.Add(new SpectrumIdentificationItemRefObj(siir, IdentData));
}
}
}
/// <summary>
/// Builds a PDH for the current protein
/// </summary>
private PSIPIanalysisprocessProteinDetectionHypothesisType BuildHypothesis( Protein p, Protein.EvidenceType ev ) {
PSIPIanalysisprocessProteinDetectionHypothesisType h = new PSIPIanalysisprocessProteinDetectionHypothesisType();
h.id = "PDH_" + p.Accession;
h.DBSequence_ref = p.DBRef;
if( p.Evidence == Protein.EvidenceType.NonConclusive || p.Evidence == Protein.EvidenceType.Filtered )
h.passThreshold = false;
else
h.passThreshold = true;
List<PeptideHypothesisType> listPeptides = new List<PeptideHypothesisType>();
foreach( Peptide f in p.Peptides ) {
PeptideHypothesisType peptide = new PeptideHypothesisType();
peptide.PeptideEvidence_Ref = f.Names[p.DBRef];
listPeptides.Add( peptide );
}
if( listPeptides.Count > 0 )
h.PeptideHypothesis = listPeptides.ToArray();
h.cvParam = new FuGECommonOntologycvParamType[1];
h.cvParam[0] = new FuGECommonOntologycvParamType(
"Protein Inference Confidence Category",
"MS:1001600", "PSI-MS" );
h.cvParam[0].value = ParseConfidence( ev );
return h;
}
