private void WriteSpectraDetails( TextWriter w, Spectrum s )
{
Tag tr = new Tag( "tr", true );
Tag td = new Tag( "td", "colspan" );
Tag th = new Tag( "th", "rowspan" );
Tag a = new Tag( "a", "href" );
int i;
w.WriteLine( "<table>\n<caption><a name=\"Spectrum"+s.ID+"\"/>Spectrum "+s.SpectrumID+"</caption>" );
w.WriteLine( tr.Render(th.Render("ID")+td.Render("3",s.SpectrumID)) );
w.WriteLine( tr.Render(th.Render("Location")+td.Render("3",s.File)) );
w.Write( tr+th.Render("PSM list")+"<td colspan=\"3\">" );
if( s.Psm.Count > 0 ) {
for( i = 0; i < s.Psm.Count-1; i++ )
w.Write( a.Render("#PSM"+s.Psm[i].ID,s.Psm[i].ID.ToString()) + ", " );
w.Write( a.Render("#PSM"+s.Psm[i].ID,s.Psm[i].ID.ToString()) );
}
w.WriteLine( "</td>"+tr );
if( s.Psm.Count == 0 ) {
w.WriteLine( "</table><br/>" );
return;
}
w.Write( tr+th.Render((s.Psm.Count*8).ToString(),"PSMs") );
bool first = true;
foreach( PSM psm in s.Psm ) {
if( first )
first = false;
else
w.Write( tr.ToString() );
w.Write( th.Render("8",psm.ID.ToString()) );
w.WriteLine( th.Render("<a name=\"PSM"+psm.ID+"\"/>Charge")+td.Render(psm.Charge.ToString())+tr );
tr.Hold = true;
w.WriteLine( tr+th.Render("M/Z")+td.Render(psm.Mz.ToString())+tr );
w.WriteLine( tr+th.Render("Rank")+td.Render(psm.Rank.ToString())+tr );
w.WriteLine( tr+th.Render("Score")+td.Render(psm.Score<0.0?"N/A":psm.Score.ToString())+tr );
w.WriteLine( tr+th.Render("Score type")+td.Render(psm.ScoreType)+tr );
w.WriteLine( tr+th.Render("Confidence")+td.Render(psm.Confidence.ToString())+tr );
w.WriteLine( tr+th.Render("PassThreshold")+td.Render(psm.passThreshold.ToString())+tr );
w.Write( tr+th.Render("Peptide")+td );
if( psm.Peptide != null ) {
w.Write( psm.Peptide.ToString() );
if( psm.Peptide.Proteins.Count > 0 ) {
w.Write( " (" );
for( i = 0; i < psm.Peptide.Proteins.Count - 1; i++ )
w.Write( a.Render("#"+psm.Peptide.Proteins[i].Accession+"__"+psm.Peptide.ID,psm.Peptide.Proteins[i].EntryEx) + ", " );
w.Write( a.Render("#"+psm.Peptide.Proteins[i].Accession+"__"+psm.Peptide.ID,psm.Peptide.Proteins[i].EntryEx) + ")" );
}
} else
w.Write( "N/A (ProCon duplicate?)" );
w.WriteLine( td.ToString()+tr);
tr.Hold = false;
}
w.WriteLine( "</table><br/>" );
w.Flush();
}
/// <summary>
/// Removes invalid PSMs and their associated peptides (if neccessary).
/// </summary>
private void FilterPsms()
{
if( Spectra.Count == 0 )
return;
List<Spectrum> spectra = new List<Spectrum>();
// Remove previous relations
foreach( Peptide f in Peptides )
f.Psm = new List<PSM>();
foreach( Spectrum spectrum in Spectra ) {
if( spectrum.Psm == null )
continue;
Spectrum tmp = null;
foreach( PSM psm in spectrum.Psm ) {
if( !CheckPsm(psm) )
continue;
if( tmp == null ) {
tmp = new Spectrum();
tmp.File = spectrum.File;
tmp.ID = spectrum.ID;
tmp.SpectrumID = spectrum.SpectrumID;
tmp.Psm = new List<PSM>();
}
tmp.Psm.Add(psm);
Peptide f = psm.Peptide;
if( !f.Psm.Contains(psm) )
f.Psm.Add(psm);
if( f.Confidence < psm.Confidence )
f.Confidence = psm.Confidence;
}
if( tmp != null )
spectra.Add(tmp);
}
Spectra = spectra;
}
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 );
}
}
}
}
