public void SetProteinRatioValid(IIdentifiedProtein ann, bool value)
{
ann.SetEnabled(value);
}
public bool IsProteinRatioValid(IIdentifiedProtein ann)
{
return(HasProteinRatio(ann) && AnnotationUtils.IsEnabled(ann, true));
}
public string GetProteinRatioDescription(IIdentifiedProtein ann, string key)
{
return(GetProteinRatioDescription(ann));
}
public bool HasProteinRatio(IIdentifiedProtein ann)
{
return(GetProteinRatioCalculator().HasProteinRatio(ann));
}
public double GetProteinRatio(IIdentifiedProtein ann, string key)
{
return(GetProteinRatio(ann));
}
public string GetProteinRatioDescription(IIdentifiedProtein ann, string key)
{
throw new NotImplementedException();
}
public double GetProteinRatio(IIdentifiedProtein ann, string key)
{
throw new NotImplementedException();
}
public void testParseFile1()
{
MascotResult mr = new MascotResultHtmlStandaloneParser(true)
.ParseFile(new FileInfo(@TestContext.CurrentContext.TestDirectory + "/../../../data//mascot_result_protein_newversion.html"));
Assert.AreEqual(33, mr.PValueScore);
Assert.AreEqual(0.05, mr.PValue);
Assert.AreEqual(IsotopicType.Monoisotopic, mr.PeakIsotopicType);
Assert.AreEqual(0.8, mr.PeakTolerance, 0.01);
Assert.AreEqual(2, mr.Count);
IIdentifiedProtein protein1 = mr[0][0];
Assert.AreEqual("sp|P00489|PHS2_RABIT", protein1.Name);
Assert.AreEqual(97610, protein1.MolecularWeight, 1.0);
Assert.AreEqual(
"Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase) - Oryctolagus cuniculus (Rabbit",
protein1.Description);
Assert.AreEqual(3, protein1.Peptides.Count);
IIdentifiedSpectrum pep11 = protein1.Peptides[0].Spectrum;
Assert.AreEqual(1053.5720, pep11.Query.ObservedMz, 0.0001);
Assert.AreEqual("Cmpd.6612.6612.1.dta", pep11.Query.FileScan.LongFileName);
Assert.AreEqual(2232, pep11.Query.QueryId);
Assert.AreEqual(1052.5647, pep11.ExperimentalMass, 0.0001);
Assert.AreEqual(1052.5654, pep11.TheoreticalMass, 0.0001);
Assert.AreEqual(0.0007, pep11.TheoreticalMinusExperimentalMass, 0.0001);
Assert.AreEqual(0, pep11.NumMissedCleavages);
Assert.AreEqual(34, pep11.Score);
Assert.AreEqual(0.039, pep11.ExpectValue);
Assert.AreEqual(1, pep11.Rank);
Assert.AreEqual("R.VIFLENYR.V", pep11.Sequence);
IIdentifiedSpectrum pep12 = protein1.Peptides[1].Spectrum;
Assert.AreEqual(527.7459, pep12.Query.ObservedMz, 0.0001);
Assert.AreEqual("Cmpd.5747.5747.2.dta", pep12.Query.FileScan.LongFileName);
Assert.AreEqual(2239, pep12.Query.QueryId);
Assert.AreEqual(1053.4772, pep12.ExperimentalMass, 0.0001);
Assert.AreEqual(1053.4767, pep12.TheoreticalMass, 0.0001);
Assert.AreEqual(-0.0005, pep12.TheoreticalMinusExperimentalMass, 0.0001);
Assert.AreEqual(0, pep12.NumMissedCleavages);
Assert.AreEqual(48, pep12.Score);
Assert.AreEqual(5.4E-5, pep12.ExpectValue, 0.001);
Assert.AreEqual(1, pep12.Rank);
Assert.AreEqual("R.TNFDAFPDK.V", pep12.Sequence);
IIdentifiedSpectrum pep13 = protein1.Peptides[2].Spectrum;
Assert.AreEqual(527.7464, pep13.Query.ObservedMz, 0.0001);
Assert.AreEqual("Cmpd.5743.5743.2.dta", pep13.Query.FileScan.LongFileName);
Assert.AreEqual(2240, pep13.Query.QueryId);
Assert.AreEqual(1053.4782, pep13.ExperimentalMass, 0.0001);
Assert.AreEqual(1053.4767, pep13.TheoreticalMass, 0.0001);
Assert.AreEqual(-0.0015, pep13.TheoreticalMinusExperimentalMass, 0.0001);
Assert.AreEqual(0, pep13.NumMissedCleavages);
Assert.AreEqual(47, pep13.Score);
Assert.AreEqual(0.0018, pep13.ExpectValue, 0.001);
Assert.AreEqual(1, pep13.Rank);
Assert.AreEqual("R.TNFDAFPDK.V", pep13.Sequence);
IIdentifiedProtein protein2 = mr[1][0];
Assert.AreEqual("REVERSED_0008631", protein2.Name);
Assert.AreEqual("", protein2.Description);
Assert.AreEqual(2, protein2.Peptides.Count);
IIdentifiedSpectrum pep21 = protein2.Peptides[0].Spectrum;
Assert.AreEqual(699.4770, pep21.Query.ObservedMz, 0.0001);
Assert.AreEqual("Standard_Protein_FIT_060222.6065.6065.1.dta", pep21.
Query.FileScan.LongFileName);
Assert.AreEqual(932, pep21.Query.QueryId);
Assert.AreEqual(698.4697, pep21.ExperimentalMass, 0.0001);
Assert.AreEqual(698.4115, pep21.TheoreticalMass, 0.0001);
Assert.AreEqual(-0.0582, pep21.TheoreticalMinusExperimentalMass, 0.0001);
Assert.AreEqual(0, pep21.NumMissedCleavages);
Assert.AreEqual(33, pep21.Score);
Assert.AreEqual(0.049, pep21.ExpectValue);
Assert.AreEqual(1, pep21.Rank);
Assert.AreEqual("R.WPAVVK.L", pep21.Sequence);
Assert.AreSame(protein1.Peptides[2], protein2.Peptides[1]);
}
public bool HasProteinRatio(IIdentifiedProtein protein)
{
return(protein.GetQuantificationItem() != null);
}
