private void LoadRelations(
SortedList<string,string> SortedAccession, SortedList<string,Peptide> SortedPeptides) {
if( m_mzid.Data.DataCollection.AnalysisData.SpectrumIdentificationList.Length != 1 )
throw new ApplicationException( "Multiple spectrum identification lists not supported" );
SortedList<string,PeptideEvidenceType> SortedEvidences = new SortedList<string, PeptideEvidenceType>();
foreach( PeptideEvidenceType evidence in m_mzid.Data.SequenceCollection.PeptideEvidence )
SortedEvidences.Add( evidence.id, evidence );
int SpectrumID = 1;
int PsmID = 1;
double score;
string type;
Peptide.ConfidenceType confidence;
foreach( SpectrumIdentificationResultType idres in
m_mzid.Data.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult ) {
Spectrum spectrum = new Spectrum();
spectrum.ID = SpectrumID++;
spectrum.File = idres.spectraData_ref;
spectrum.SpectrumID = idres.spectrumID;
spectrum.Psm = new List<PSM>();
Spectra.Add(spectrum);
foreach( SpectrumIdentificationItemType item in idres.SpectrumIdentificationItem ) {
//Console.Out.WriteLine(item.id);
GetPsmScore( item, out score, out type, out confidence );
PSM psm = new PSM();
psm.ID = PsmID++;
psm.Charge = item.chargeState;
psm.Mz = item.experimentalMassToCharge;
psm.Rank = item.rank;
psm.Score = score;
psm.ScoreType = type;
psm.Confidence = confidence;
psm.passThreshold = item.passThreshold;
psm.Spectrum = spectrum;
spectrum.Psm.Add(psm);
if( item.PeptideEvidenceRef == null )
continue;
foreach( PeptideEvidenceRefType evref in item.PeptideEvidenceRef ) {
//Console.Out.WriteLine(evref.peptideEvidence_ref);
PeptideEvidenceType evidence = SortedEvidences[evref.peptideEvidence_ref];
Peptide pep = SortedPeptides[evidence.peptide_ref];
if( pep.Sequence == null || pep.Sequence.Length == 0 ) { // ProCon 0.9.348 bug
//Notify( "Skiped peptide with empty sequence: " + pep.DBRef );
continue;
}
pep.Decoy = evidence.isDecoy;
psm.Peptide = pep;
//pep.Psm.Add(psm);
Protein prot = m_SortedProteins[SortedAccession[evidence.dBSequence_ref]];
if( pep.Proteins.Contains(prot) )
continue;
prot.Peptides.Add( pep );
pep.Proteins.Add( prot );
}
}
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pe"></param>
/// <param name="idata"></param>
public PeptideEvidenceObj(PeptideEvidenceType pe, IdentDataObj idata)
: base(pe, idata)
{
DBSequenceRef = pe.dBSequence_ref;
PeptideRef = pe.peptide_ref;
_start = pe.start;
StartSpecified = pe.startSpecified;
_end = pe.end;
EndSpecified = pe.endSpecified;
Pre = pe.pre;
Post = pe.post;
TranslationTableRef = pe.translationTable_ref;
_frame = pe.frame;
FrameSpecified = pe.frameSpecified;
IsDecoy = pe.isDecoy;
Id = pe.id;
Name = pe.name;
}