private void WriteProteinList( TextWriter w, Tag tr, Protein.EvidenceType evidence ) {
Tag a = new Tag( evidence == Protein.EvidenceType.Filtered ? null : "a", "href" );
Tag td = new Tag( "td" );
Tag tdr = new Tag( "td", "rowspan" );
Tag tdc = new Tag( "td", "colspan" );
foreach( Protein p in Proteins ) {
if( p.Evidence != evidence )
continue;
if( p.Subset.Count == 0 ) {
w.Write( tr.Render(
td.Render(a.Render("#"+p.Accession,p.EntryEx))+
td.Render(p.Evidence.ToString())+
tdc.Render("2",Peptides2Html(p))+
td.Render(p.Desc) ));
continue;
}
w.WriteLine( tr.Render(
tdr.Render(p.Subset.Count.ToString(),p.Entry)+
tdr.Render(p.Subset.Count.ToString(),p.Evidence.ToString())+
td.Render(a.Render("#"+p.Subset[0].Accession,p.Subset[0].EntryEx)+": ")+
td.Render(Peptides2Html(p.Subset[0]))+
td.Render(p.Subset[0].Desc) ));
tr.Hold = true;
for( int i = 1; i < p.Subset.Count; i++ )
w.WriteLine( tr.Render(
td.Render(a.Render("#"+p.Subset[i].Accession,p.Subset[i].EntryEx)+": ")+
td.Render(Peptides2Html(p.Subset[i]))+
td.Render(p.Subset[i].Desc) ));
tr.Hold = false;
}
}
private void WriteProteinDetails( TextWriter w, Protein.EvidenceType evidence ) {
foreach( Protein p in Proteins ) {
if( p.Evidence != evidence )
continue;
if( p.Subset.Count == 0 ) {
WriteProteinDetails( w, p );
continue;
}
foreach( Protein p2 in p.Subset )
WriteProteinDetails( w, p2 );
}
}
private void UpdatePdhCvs(ProteinDetectionHypothesisType pdh, Protein.EvidenceType evidence)
{
List <AbstractParamType> list = new List <AbstractParamType>();
foreach (AbstractParamType item in pdh.Items)
{
if (!item.name.Contains("PAnalyzer") && !item.name.Contains("leading"))
{
list.Add(item);
}
}
CVParamType ev = new CVParamType(), ld = new CVParamType();
ev.cvRef = "PSI-MS";
ld.cvRef = "PSI-MS";
switch (evidence)
{
case Protein.EvidenceType.Conclusive:
ev.accession = "MS:1002213";
ev.name = "PAnalyzer:conclusive protein";
ld.accession = "MS:1002401";
ld.name = "leading protein";
break;
case Protein.EvidenceType.Indistinguishable:
ev.accession = "MS:1002214";
ev.name = "PAnalyzer:indistinguishable protein";
ld.accession = "MS:1002401";
ld.name = "leading protein";
break;
case Protein.EvidenceType.Group:
ev.accession = "MS:1002216";
ev.name = "PAnalyzer:ambiguous group member";
ld.accession = "MS:1002401";
ld.name = "leading protein";
break;
case Protein.EvidenceType.NonConclusive:
ev.accession = "MS:1002215";
ev.name = "PAnalyzer:non-conclusive protein";
ld.accession = "MS:1002402";
ld.name = "non-leading protein";
break;
default: // filtered
return;
}
list.Add(ld);
list.Add(ev);
pdh.Items = list.ToArray();
}
/// <summary>
/// Parses the confidence enum to a string.
/// </summary>
public string ParseConfidence( Protein.EvidenceType e ) {
switch( e ) {
case Protein.EvidenceType.Conclusive:
return "conclusive";
case Protein.EvidenceType.Group:
return "ambiguous group";
case Protein.EvidenceType.Indistinguishable:
return "indistinguishable";
case Protein.EvidenceType.NonConclusive:
return "non conclusive";
}
return e.ToString();
}
/// <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;
}
