// TODO: Support empty PDH in input mzid
protected virtual List<ProteinAmbiguityGroupType> BuildProteinDetectionList()
{
int gid = 1;
SortedList<string,ProteinDetectionHypothesisType> list = new SortedList<string, ProteinDetectionHypothesisType>();
List<ProteinAmbiguityGroupType> groups = new List<ProteinAmbiguityGroupType>();
foreach( ProteinAmbiguityGroupType grp in m_mzid.Data.DataCollection.AnalysisData.ProteinDetectionList.ProteinAmbiguityGroup )
foreach( ProteinDetectionHypothesisType pdh in grp.ProteinDetectionHypothesis )
list.Add( pdh.dBSequence_ref, pdh );
foreach( Protein p in Proteins ) {
ProteinAmbiguityGroupType g = new ProteinAmbiguityGroupType();
CVParamType ev = new CVParamType();
ev.accession = "MS:1001600";
ev.cvRef = "PSI-MS";
ev.name = "Protein Inference Confidence Category";
switch( p.Evidence ) {
case Protein.EvidenceType.Conclusive:
ev.value = "conclusive"; break;
case Protein.EvidenceType.Indistinguishable:
ev.value = "indistinguishable"; break;
case Protein.EvidenceType.Group:
ev.value = "ambiguous group"; break;
case Protein.EvidenceType.NonConclusive:
ev.value = "non conclusive"; break;
default:
continue;
}
g.id = "PAG_" + gid; gid++;
if( p.Subset.Count == 0 ) {
//g.ProteinDetectionHypothesis.Add(list[p.DBRef]);
g.ProteinDetectionHypothesis = new ProteinDetectionHypothesisType[]{list[p.DBRef]};
g.Items = new CVParamType[]{ev};
} else {
List<ProteinDetectionHypothesisType> listpdh = new List<ProteinDetectionHypothesisType>();
foreach( Protein p2 in p.Subset ) {
ProteinDetectionHypothesisType pdh = list[p2.DBRef];
pdh.Items = new CVParamType[]{ev};
listpdh.Add( pdh );
}
g.ProteinDetectionHypothesis = listpdh.ToArray();
}
groups.Add( g );
}
return groups;
}
private List<ProteinAmbiguityGroupType> BuildPags()
{
int gid = 1;
SortedList<string,ProteinDetectionHypothesisType> listPdh = new SortedList<string, ProteinDetectionHypothesisType>();
SortedList<string,ProteinAmbiguityGroupType> listPag = new SortedList<string, ProteinAmbiguityGroupType>();
List<ProteinAmbiguityGroupType> groups = new List<ProteinAmbiguityGroupType>();
// Collect existing PDHs
foreach( ProteinAmbiguityGroupType grp in m_mzid.Data.DataCollection.AnalysisData.ProteinDetectionList.ProteinAmbiguityGroup )
foreach( ProteinDetectionHypothesisType pdh in grp.ProteinDetectionHypothesis )
if( !listPdh.ContainsKey(pdh.dBSequence_ref) )
listPdh.Add( pdh.dBSequence_ref, pdh );
// Build PAGs for every group except non-conclusive proteins
foreach( Protein p in Proteins ) {
if( p.Evidence == Protein.EvidenceType.NonConclusive || p.Evidence == Protein.EvidenceType.Filtered )
continue;
ProteinAmbiguityGroupType g = new ProteinAmbiguityGroupType();
g.id = "PAG_" + gid++;
if( p.Subset.Count == 0 ) {
g.ProteinDetectionHypothesis = new ProteinDetectionHypothesisType[]{listPdh[p.DBRef]};
UpdatePdhCvs(g.ProteinDetectionHypothesis[0],p.Evidence);
listPag.Add(g.ProteinDetectionHypothesis[0].dBSequence_ref,g);
} else {
List<ProteinDetectionHypothesisType> tmp = new List<ProteinDetectionHypothesisType>();
foreach( Protein p2 in p.Subset ) {
ProteinDetectionHypothesisType pdh = listPdh[p2.DBRef];
UpdatePdhCvs(pdh,p2.Evidence);
tmp.Add( pdh );
listPag.Add(pdh.dBSequence_ref,g);
}
g.ProteinDetectionHypothesis = tmp.ToArray();
}
groups.Add( g );
}
// Include non-conclusive proteins in existing PAGs
bool include;
foreach( Protein p in Proteins ) {
if( p.Evidence != Protein.EvidenceType.NonConclusive )
continue;
ProteinDetectionHypothesisType pdh = listPdh[p.DBRef];
UpdatePdhCvs(pdh, Protein.EvidenceType.NonConclusive);
foreach( Peptide f in p.Peptides )
foreach( Protein t in f.Proteins ) {
include = true;
if( !listPag.ContainsKey(t.DBRef) )
continue;
ProteinAmbiguityGroupType g = listPag[t.DBRef];
foreach( ProteinDetectionHypothesisType h in g.ProteinDetectionHypothesis )
if( GetBaseId(h) == GetBaseId(pdh) ) {
include = false;
break;
}
if( include ) {
ProteinDetectionHypothesisType clon = ClonePDH(pdh);
clon.id = GetBaseId(clon)+"@"+g.id;
List<ProteinDetectionHypothesisType> tmp =
new List<ProteinDetectionHypothesisType>(g.ProteinDetectionHypothesis);
tmp.Add(clon);
g.ProteinDetectionHypothesis = tmp.ToArray();
}
}
}
return groups;
}
