//[Test]
public void Test()
{
PFindSpectrumParser parser = new PFindSpectrumParser();
var peptides = parser.ReadFromFile(fileName);
Assert.AreEqual(2970, peptides.Count);
Assert.AreEqual(1, peptides[0].Query.QueryId);
Assert.AreEqual("B06-11073.1000.1000.2.dta", peptides[0].Query.FileScan.LongFileName);
Assert.AreEqual(2, peptides[0].Query.Charge);
//Assert.AreEqual(1, peptides[0].NumMissedCleavages);
Assert.AreEqual(839.49962, peptides[0].ExperimentalMH, 0.00001);
Assert.AreEqual(420.25345, peptides[0].ObservedMz, 0.00001);
Assert.AreEqual(54.08608, peptides[0].Score, 0.00001);
Assert.AreEqual(1.537127E-001, peptides[0].ExpectValue, 0.0000001);
Assert.AreEqual(839.46214, peptides[0].TheoreticalMH, 0.00001);
Assert.AreEqual(1, peptides[0].Proteins.Count);
Assert.AreEqual("YFR023W", peptides[0].Proteins[0]);
Assert.AreEqual("YSISNKK", peptides[0].Sequence);
Assert.AreEqual("", peptides[0].Modifications);
Assert.AreEqual(1.0, peptides[0].DeltaScore, 0.01);
var pep = peptides.Find(m => m.Query.QueryId == 32);
Assert.AreEqual("B06-11073.1061.1061.2.dta", pep.Query.FileScan.LongFileName);
Assert.AreEqual("Oxidation_M", pep.Modifications);
Assert.AreEqual("IM*AGFKDDTK", pep.Sequence);
Assert.AreEqual(0.044, pep.DeltaScore, 0.001);
}
protected override ISpectrumParser GetSpectrumParser()
{
var result = new PFindSpectrumParser(options.GetTitleParser());
result.Progress = Progress;
return(result);
}
protected override string GetTitleSample()
{
if (datFiles.SelectFileNames.Length > 0)
{
return(PFindSpectrumParser.GetTitleSample(datFiles.SelectFileNames[0]));
}
else if (datFiles.FileNames.Length > 0)
{
return(PFindSpectrumParser.GetTitleSample(datFiles.FileNames[0]));
}
return(base.GetTitleSample());
}
//[Test]
public void TestParseModification()
{
PFindSpectrumParser parser = new PFindSpectrumParser();
var sec = new Dictionary<string, string>();
sec.Add("Fixed_modifications", "1,Carbamidomethyl_C");
sec.Add("Variable_modifications", "2,Oxidation_M,Phosphylation_STY");
var mods = parser.ParseModification(sec);
Assert.AreEqual(1, mods.StaticModification.Count);
Assert.AreEqual("C", mods.StaticModification[0].Aminoacid);
Assert.AreEqual("Carbamidomethyl", mods.StaticModification[0].Modification);
Assert.AreEqual(2, mods.DynamicModification.Count);
Assert.AreEqual("M", mods.DynamicModification[0].Aminoacid);
Assert.AreEqual("Oxidation", mods.DynamicModification[0].Modification);
Assert.AreEqual("STY", mods.DynamicModification[1].Aminoacid);
Assert.AreEqual("Phosphylation", mods.DynamicModification[1].Modification);
}
