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;
}
}
}
protected bool CheckPsm( bool passThreshold, int rank, Peptide.ConfidenceType confidence, double score, string type ) {
if( RequirePassTh && !passThreshold )
return false;
if( RankThreshold != 0 && (rank == 0 || rank > RankThreshold) )
return false;
if( Type >= SourceType.mzIdentML110 && Type <= SourceType.mzIdentML120 && (int)confidence < (int)SeqThreshold )
return false;
if( type == "Mascot expectation value" && score > MascotThreshold )
return false;
if( type == "X!Tandem expect" && score > XTandemThreshold )
return false;
return true;
}
/// <summary>
/// Default constructor
/// </summary>
public Mapper( Software sw )
{
m_Software = sw;
Proteins = new List<Protein>();
Peptides = new List<Peptide>();
Spectra = new List<Spectrum>();
m_Stats = new StatsStruct();
m_Format = new System.Globalization.NumberFormatInfo();
m_Format.NumberDecimalSeparator = ".";
m_Run = 0;
m_Type = SourceType.Unknown;
LengthThreshold = 0;
PlgsThreshold = Peptide.ConfidenceType.NoThreshold;
SeqThreshold = Peptide.ConfidenceType.NoThreshold;
XTandemThreshold = 0.05;
XTandemAvailable = false;
MascotThreshold = 0.05;
MascotAvailable = false;
RequirePassTh = true;
RankThreshold = 0;
FilterDecoys = true;
RunsThreshold = 1;
m_InputFiles = new List<string>();
}
