public void TestKeepDistinctPeptideOnly()
{
var spectrum1 = new IdentifiedSpectrum();
var pep1 = spectrum1.NewPeptide();
var spectrum2 = new IdentifiedSpectrum();
var pep2 = spectrum2.NewPeptide();
var spectrum3 = new IdentifiedSpectrum();
var pep3 = spectrum3.NewPeptide();
var spectrum4 = new IdentifiedSpectrum();
var pep4 = spectrum4.NewPeptide();
var protein1 = new IdentifiedProtein();
protein1.Peptides.Add(pep1);
protein1.Peptides.Add(pep2);
var protein2 = new IdentifiedProtein();
protein2.Peptides.Add(pep1);
protein2.Peptides.Add(pep3);
var protein3 = new IdentifiedProtein();
protein3.Peptides.Add(pep2);
protein3.Peptides.Add(pep4);
var g1 = new IdentifiedProteinGroup();
g1.Add(protein1);
var g2 = new IdentifiedProteinGroup();
g2.Add(protein2);
var g3 = new IdentifiedProteinGroup();
g3.Add(protein3);
IIdentifiedResult ir = new IdentifiedResult();
ir.Add(g1);
ir.Add(g2);
ir.Add(g3);
new DistinctResultDistiller().KeepDistinctPeptideOnly(ir);
Assert.AreEqual(2, ir.Count);
Assert.AreEqual(g2, ir[0]);
Assert.AreEqual(g3, ir[1]);
Assert.AreEqual(1, ir[0].GetPeptides().Count);
Assert.AreEqual(spectrum3, ir[0].GetPeptides()[0]);
Assert.AreEqual(1, ir[1].GetPeptides().Count);
Assert.AreEqual(spectrum4, ir[1].GetPeptides()[0]);
}
public void TestKeepDistinctPeptideOnly()
{
var spectrum1 = new IdentifiedSpectrum();
var pep1 = spectrum1.NewPeptide();
var spectrum2 = new IdentifiedSpectrum();
var pep2 = spectrum2.NewPeptide();
var spectrum3 = new IdentifiedSpectrum();
var pep3 = spectrum3.NewPeptide();
var spectrum4 = new IdentifiedSpectrum();
var pep4 = spectrum4.NewPeptide();
var protein1 = new IdentifiedProtein();
protein1.Peptides.Add(pep1);
protein1.Peptides.Add(pep2);
var protein2 = new IdentifiedProtein();
protein2.Peptides.Add(pep1);
protein2.Peptides.Add(pep3);
var protein3 = new IdentifiedProtein();
protein3.Peptides.Add(pep2);
protein3.Peptides.Add(pep4);
var g1 = new IdentifiedProteinGroup();
g1.Add(protein1);
var g2 = new IdentifiedProteinGroup();
g2.Add(protein2);
var g3 = new IdentifiedProteinGroup();
g3.Add(protein3);
IIdentifiedResult ir = new IdentifiedResult();
ir.Add(g1);
ir.Add(g2);
ir.Add(g3);
new DistinctResultDistiller().KeepDistinctPeptideOnly(ir);
Assert.AreEqual(2, ir.Count);
Assert.AreEqual(g2, ir[0]);
Assert.AreEqual(g3, ir[1]);
Assert.AreEqual(1, ir[0].GetPeptides().Count);
Assert.AreEqual(spectrum3, ir[0].GetPeptides()[0]);
Assert.AreEqual(1, ir[1].GetPeptides().Count);
Assert.AreEqual(spectrum4, ir[1].GetPeptides()[0]);
}
private IIdentifiedSpectrum ParsePeptide(string line)
{
IIdentifiedSpectrum result = new IdentifiedSpectrum();
string[] parts = line.Split(splits);
result.Query.FileScan.Experimental = parts[bestLocalizationRawFileIndex];
result.Query.FileScan.FirstScan = int.Parse(parts[bestLocalizationScanNumberIndex]);
result.Query.FileScan.LastScan = result.Query.FileScan.FirstScan;
result.Query.FileScan.Charge = int.Parse(parts[chargeIndex]);
result.Score = MyConvert.ToDouble(parts[scoreIndex]);
result.DeltaScore = MyConvert.ToDouble(parts[scoreDiffIndex]);
result.ExpectValue = MyConvert.ToDouble(parts[pepIndex]);
result.Probability = MyConvert.ToDouble(parts[localizationProbIndex]);
string seq = parts[sequenceWindowIndex];
string modifications = parts[modificationWindowIndex];
seq = GetModifiedSequence(seq, modifications);
seq = seq.Replace("_", "");
Match m = modReg.Match(seq);
if (m.Success)
{
while (m.Success)
{
string mod = m.Groups[1].Value;
if (!modCharMap.ContainsKey(mod))
{
modCharMap[mod] = ModificationConsts.MODIFICATION_CHAR.Substring(modCharMap.Count + 1, 1);
}
m = m.NextMatch();
}
seq = ReplaceModificationStringToChar(seq);
}
result.NewPeptide().Sequence = seq;
StringBuilder sb = new StringBuilder();
foreach (var mod in modCharMap)
{
if (seq.Contains(mod.Value))
{
sb.Append(MyConvert.Format("{0}={1};", mod.Value, mod.Key));
}
}
result.Modifications = sb.ToString();
return(result);
}