private void GetPsmScore(
SpectrumIdentificationItemType item,
out double score, out string type, out Peptide.ConfidenceType confidence ) {
score = -1.0;
type = "N/A";
confidence = item.passThreshold ? Peptide.ConfidenceType.PassThreshold : Peptide.ConfidenceType.NoThreshold;
if( item.Items == null )
return;
foreach( AbstractParamType param in item.Items ) {
if( !(param is CVParamType) )
continue;
CVParamType cv = param as CVParamType;
if( cv.accession == "MS:1001155" ) {
score = double.Parse(cv.value, m_Format);
type = "ProteomeDiscoverer/SEQUEST Confidence XCorr";
if( score >= m_GreenTh[item.chargeState-1] )
confidence = Peptide.ConfidenceType.Green;
else if( score >= m_YellowTh[item.chargeState-1] )
confidence = Peptide.ConfidenceType.Yellow;
else
confidence = Peptide.ConfidenceType.Red;
break;
} else if( cv.accession == "MS:1001172" ) {
score = double.Parse(cv.value, m_Format);
type = "Mascot expectation value";
break;
} else if( cv.accession == "MS:1001330" ) {
score = double.Parse( cv.value, m_Format );
type = "X!Tandem expect";
break;
}
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sii"></param>
/// <param name="idata"></param>
public SpectrumIdentificationItemObj(SpectrumIdentificationItemType sii, IdentDataObj idata)
: base(sii, idata)
{
Id = sii.id;
Name = sii.name;
ChargeState = sii.chargeState;
ExperimentalMassToCharge = sii.experimentalMassToCharge;
_calculatedMassToCharge = sii.calculatedMassToCharge;
CalculatedMassToChargeSpecified = sii.calculatedMassToChargeSpecified;
_calculatedPI = sii.calculatedPI;
CalculatedPISpecified = sii.calculatedPISpecified;
PeptideRef = sii.peptide_ref;
Rank = sii.rank;
PassThreshold = sii.passThreshold;
MassTableRef = sii.massTable_ref;
SampleRef = sii.sample_ref;
PeptideEvidences = new IdentDataList <PeptideEvidenceRefObj>(1);
Fragmentations = new IdentDataList <IonTypeObj>(1);
if (sii.PeptideEvidenceRef?.Count > 0)
{
PeptideEvidences.AddRange(sii.PeptideEvidenceRef, pe => new PeptideEvidenceRefObj(pe, IdentData));
}
if (sii.Fragmentation?.Count > 0)
{
Fragmentations.AddRange(sii.Fragmentation, f => new IonTypeObj(f, IdentData));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sii"></param>
/// <param name="idata"></param>
public SpectrumIdentificationItemObj(SpectrumIdentificationItemType sii, IdentDataObj idata)
: base(sii, idata)
{
Id = sii.id;
Name = sii.name;
ChargeState = sii.chargeState;
ExperimentalMassToCharge = sii.experimentalMassToCharge;
_calculatedMassToCharge = sii.calculatedMassToCharge;
CalculatedMassToChargeSpecified = sii.calculatedMassToChargeSpecified;
_calculatedPI = sii.calculatedPI;
CalculatedPISpecified = sii.calculatedPISpecified;
PeptideRef = sii.peptide_ref;
Rank = sii.rank;
PassThreshold = sii.passThreshold;
MassTableRef = sii.massTable_ref;
SampleRef = sii.sample_ref;
_peptideEvidences = null;
_fragmentations = null;
if ((sii.PeptideEvidenceRef != null) && (sii.PeptideEvidenceRef.Count > 0))
{
PeptideEvidences = new IdentDataList <PeptideEvidenceRefObj>();
foreach (var pe in sii.PeptideEvidenceRef)
{
PeptideEvidences.Add(new PeptideEvidenceRefObj(pe, IdentData));
}
}
if ((sii.Fragmentation != null) && (sii.Fragmentation.Count > 0))
{
Fragmentations = new IdentDataList <IonTypeObj>();
foreach (var f in sii.Fragmentation)
{
Fragmentations.Add(new IonTypeObj(f, IdentData));
}
}
}
