public void TestSameEngineDifferentParameters()
{
ClassificationOptions co = new ClassificationOptions();
co.ClassifyByCharge = true;
co.ClassifyByMissCleavage = true;
co.ClassifyByModification = true;
co.ModifiedAminoacids = "STY";
co.ClassifyByNumProteaseTermini = true;
var s1 = new MascotPeptideTextFormat().ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/deisotopic.peptides");
IdentifiedSpectrumUtils.RemoveSpectrumWithAmbigiousAssignment(s1);
s1.ForEach(m => m.Tag = "deisotopic");
var s2 = new MascotPeptideTextFormat().ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/deisotopic-top10.peptides");
IdentifiedSpectrumUtils.RemoveSpectrumWithAmbigiousAssignment(s2);
s2.ForEach(m => m.Tag = "deisotopic-top");
var all = s1.Union(s2).ToList();
var p1 = new List <IIdentifiedSpectrum>(all);
IdentifiedSpectrumUtils.KeepTopPeptideFromSameEngineDifferentParameters(p1, new ScoreFunction());
p1.ForEach(m => m.ClassificationTag = "deisotopic/deisotopic-top");
var bin1 = co.BuildSpectrumBin(p1);
var p2 = new List <IIdentifiedSpectrum>(all);
IdentifiedSpectrumUtils.KeepUnconflictPeptidesFromSameEngineDifferentParameters(p2, new ScoreFunction());
p2.ForEach(m => m.ClassificationTag = "deisotopic/deisotopic-top");
var bin2 = co.BuildSpectrumBin(p2);
bin2.ForEach(m =>
{
IdentifiedSpectrumUtils.KeepTopPeptideFromSameEngineDifferentParameters(m.Spectra, new ScoreFunction());
var n = bin1.Find(a => a.Condition.ToString().Equals(m.Condition.ToString()));
Assert.AreEqual(m.Spectra.Count, n.Spectra.Count);
//{
// if (m.Condition.ToString().Equals("deisotopic/deisotopic-top; Charge=2; MissCleavage=0; Modification=1; NumProteaseTermini=2"))
// {
// Assert.IsTrue(n.Spectra.Any(k => k.Query.FileScan.ShortFileName.Equals("20111128_CLi_v_4-2k_2mg_TiO2_iTRAQ,4992")));
// }
// var diff1 = m.Spectra.Except(n.Spectra).ToList();
// Console.WriteLine(m.Condition.ToString() + " : " + diff1.Count.ToString());
// diff1.ForEach(k =>
// {
// var lst = all.FindAll(l => l.Query.FileScan.LongFileName.Equals(k.Query.FileScan.LongFileName));
// lst.ForEach(q => Console.WriteLine(q.Query.FileScan.ShortFileName + "\t" + q.Tag + "\t" + q.Score.ToString() + "\t" + q.Sequence));
// });
//}
});
}
public void TestSameEngineDifferentParameters()
{
ClassificationOptions co = new ClassificationOptions();
co.ClassifyByCharge = true;
co.ClassifyByMissCleavage = true;
co.ClassifyByModification = true;
co.ModifiedAminoacids = "STY";
co.ClassifyByNumProteaseTermini = true;
var s1 = new MascotPeptideTextFormat().ReadFromFile(@"../../../data/deisotopic.peptides");
IdentifiedSpectrumUtils.RemoveSpectrumWithAmbigiousAssignment(s1);
s1.ForEach(m => m.Tag = "deisotopic");
var s2 = new MascotPeptideTextFormat().ReadFromFile(@"../../../data/deisotopic-top10.peptides");
IdentifiedSpectrumUtils.RemoveSpectrumWithAmbigiousAssignment(s2);
s2.ForEach(m => m.Tag = "deisotopic-top");
var all = s1.Union(s2).ToList();
var p1 = new List<IIdentifiedSpectrum>(all);
IdentifiedSpectrumUtils.KeepTopPeptideFromSameEngineDifferentParameters(p1, new ScoreFunction());
p1.ForEach(m => m.ClassificationTag = "deisotopic/deisotopic-top");
var bin1 = co.BuildSpectrumBin(p1);
var p2 = new List<IIdentifiedSpectrum>(all);
IdentifiedSpectrumUtils.KeepUnconflictPeptidesFromSameEngineDifferentParameters(p2, new ScoreFunction());
p2.ForEach(m => m.ClassificationTag = "deisotopic/deisotopic-top");
var bin2 = co.BuildSpectrumBin(p2);
bin2.ForEach(m =>
{
IdentifiedSpectrumUtils.KeepTopPeptideFromSameEngineDifferentParameters(m.Spectra, new ScoreFunction());
var n = bin1.Find(a => a.Condition.ToString().Equals(m.Condition.ToString()));
Assert.AreEqual(m.Spectra.Count, n.Spectra.Count);
//{
// if (m.Condition.ToString().Equals("deisotopic/deisotopic-top; Charge=2; MissCleavage=0; Modification=1; NumProteaseTermini=2"))
// {
// Assert.IsTrue(n.Spectra.Any(k => k.Query.FileScan.ShortFileName.Equals("20111128_CLi_v_4-2k_2mg_TiO2_iTRAQ,4992")));
// }
// var diff1 = m.Spectra.Except(n.Spectra).ToList();
// Console.WriteLine(m.Condition.ToString() + " : " + diff1.Count.ToString());
// diff1.ForEach(k =>
// {
// var lst = all.FindAll(l => l.Query.FileScan.LongFileName.Equals(k.Query.FileScan.LongFileName));
// lst.ForEach(q => Console.WriteLine(q.Query.FileScan.ShortFileName + "\t" + q.Tag + "\t" + q.Score.ToString() + "\t" + q.Sequence));
// });
//}
});
}
