public void AddPsm(PSM psm)
{
if (BestMatch == null)
{
BestMatch = psm;
}
else
{
if (psm.Score < BestMatch.Score)
{
BestMatch = psm;
}
else if (psm.Score.FussyEquals(BestMatch.Score))
{
if (Math.Abs(psm.CorrectedPrecursorMassError) < CorrectedPrecursorErrorPPM)
{
BestMatch = psm;
}
}
}
// Be conservative, if the peptide sequence is both forward and decoy, favor decoy
if (psm.IsDecoy)
{
IsDecoy = true;
}
PSMs.Add(psm);
}
public void Read(IList <Modification> fixedModifications, int numberOfTopHits = 1, bool higherScoresAreBetter = false)
{
_data.Clear();
bool first = true;
using (CsvReader reader = new CsvReader(new StreamReader(FilePath), true))
{
string[] headers = reader.GetFieldHeaders();
HasPPMInfo = headers.Contains("Precursor Mass Error (ppm)");
while (reader.ReadNextRecord())
{
if (first)
{
RawFileName = reader["Filename/id"].Split('.')[0];
first = false;
}
int scanNumber = int.Parse(reader["Spectrum number"]);
PSM psm = new PSM(scanNumber)
{
Score = double.Parse(reader["E-value"])
};
SortedMaxSizedContainer <PSM> peptides;
if (!_data.TryGetValue(scanNumber, out peptides))
{
peptides = new SortedMaxSizedContainer <PSM>(numberOfTopHits);
_data.Add(scanNumber, peptides);
}
if (!peptides.Add(psm))
{
continue;
}
psm.FileName = reader["Filename/id"];
psm.Charge = int.Parse(reader["Charge"]);
psm.IsDecoy = reader["Defline"].StartsWith("DECOY_");
if (HasPPMInfo)
{
psm.PrecursorMassError = double.Parse(reader["Precursor Mass Error (ppm)"]);
}
psm.SetSequenceAndMods(reader["Peptide"].ToUpper(), fixedModifications, reader["Mods"]);
}
}
PeptideSpectralMatches.Clear();
foreach (SortedMaxSizedContainer <PSM> set in _data.Values)
{
PeptideSpectralMatches.AddRange(set);
}
}
public int CompareTo(PSM other)
{
return(Score.CompareTo(other.Score));
}
public Peptide(PSM psm)
{
PSMs = new List <PSM>();
IsDecoy = false;
AddPsm(psm);
}