public void TestUniqueCount()
{
var protein = new IdentifiedProtein();
var spectrum = new IdentifiedSpectrum();
var peptides = new List <IIdentifiedPeptide>();
peptides.Add(new IdentifiedPeptide(spectrum)
{
Sequence = "ILLLAR"
});
peptides.Add(new IdentifiedPeptide(spectrum)
{
Sequence = "LILIAR"
});
Assert.AreEqual(1, IdentifiedPeptideUtils.GetUniquePeptideCount(peptides));
peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum())
{
Sequence = "LIIIAR"
});
Assert.AreEqual(1, IdentifiedPeptideUtils.GetUniquePeptideCount(peptides));
}
private IIdentifiedSpectrum ReadIndividualPeptide(XmlTextReader reader, string protein)
{
IIdentifiedSpectrum result = new IdentifiedSpectrum();
Dictionary <string, string> elements = new Dictionary <string, string>();
String nodeName = "";
while (reader.Read())
{
switch (reader.NodeType)
{
case XmlNodeType.Element:
nodeName = reader.Name;
break;
case XmlNodeType.Text:
elements.Add(nodeName, reader.Value);
break;
case XmlNodeType.EndElement:
if (reader.Name.Equals(peptideTag))
{
AssignPeptideValue(result, elements, protein);
return(result);
}
break;
}
}
return(result);
}
public void TestFilter2()
{
var spectrum = new IdentifiedSpectrum();
spectrum.Query.FileScan.LongFileName = "ABDCDD.12.123.2.dat";
var pro1 = new IdentifiedProtein("P1");
pro1.Peptides.Add(new IdentifiedPeptide(spectrum)
{
Sequence = "AAAAAAA"
});
var pro2 = new IdentifiedProtein("P2");
pro2.Peptides.Add(new IdentifiedPeptide(spectrum)
{
Sequence = "BBBBBBB"
});
var g1 = new IdentifiedProteinGroup();
g1.Add(pro1);
g1.Add(pro2);
IdentifiedResult ir = new IdentifiedResult();
ir.Add(g1);
Assert.AreEqual(1, ir.Count);
Assert.AreEqual(2, ir[0].Count);
Assert.AreEqual(1, ir.GetSpectra().Count);
ir.Filter(m =>
{
return(m.Sequence.Contains('A'));
});
Assert.AreEqual(1, ir.Count);
Assert.AreEqual(1, ir[0].Count);
Assert.AreEqual(1, ir.GetSpectra().Count);
Assert.AreSame(pro1, ir[0][0]);
ir.Filter(m =>
{
return(m.Sequence.Contains('C'));
});
Assert.AreEqual(0, ir.Count);
}
public void TestDistinctPeptides()
{
IdentifiedProtein protein = new IdentifiedProtein();
IdentifiedSpectrum sp1 = new IdentifiedSpectrum();
IdentifiedSpectrum sp2 = new IdentifiedSpectrum();
protein.Peptides.Add(new IdentifiedPeptide(sp1));
protein.Peptides.Add(new IdentifiedPeptide(sp1));
protein.Peptides.Add(new IdentifiedPeptide(sp2));
Assert.AreEqual(3, protein.Peptides.Count);
Assert.AreEqual(2, protein.GetSpectra().Count);
Assert.AreEqual(2, protein.GetDistinctPeptides().Count());
}
public void TestSort()
{
IdentifiedSpectrum sp1 = new IdentifiedSpectrum();
sp1.Query.FileScan.LongFileName = "YEAST_0612_G1_SAX_080806_09.17702.17702.2.out";
new IdentifiedPeptide(sp1)
{
Sequence = "K.GFFSFATQK.L"
};
IdentifiedSpectrum sp2 = new IdentifiedSpectrum();
sp2.Query.FileScan.LongFileName = "YEAST_0612_G1_SAX_080806_09.17707.17708.1.out";
new IdentifiedPeptide(sp2)
{
Sequence = "K.GFFSFATQK.L"
};
IdentifiedSpectrum sp3 = new IdentifiedSpectrum();
sp3.Query.FileScan.LongFileName = "YEAST_0612_G1_SAX_080806_09.7707.7708.2.out";
new IdentifiedPeptide(sp3)
{
Sequence = "K.GFFSFATQK.L"
};
IdentifiedSpectrum sp4 = new IdentifiedSpectrum();
sp4.Query.FileScan.LongFileName = "YEAST_0612_G1_SAX_080806_09.7707.7708.2.out";
new IdentifiedPeptide(sp4)
{
Sequence = "K.AAAAAAAK.L"
};
List <IIdentifiedSpectrum> spectra = new List <IIdentifiedSpectrum>();
spectra.Add(sp2);
spectra.Add(sp1);
spectra.Add(sp3);
spectra.Add(sp4);
spectra.Sort();
Assert.AreSame(sp4, spectra[0]);
Assert.AreSame(sp3, spectra[1]);
Assert.AreSame(sp1, spectra[2]);
Assert.AreSame(sp2, spectra[3]);
}
public void TestCalculateCoverage()
{
IdentifiedProtein protein = new IdentifiedProtein();
//total 30 amino acids
protein.Sequence = "ABCDEDFDEFDSESLKJFDJLSLGFGDDGD";
IdentifiedSpectrum s1 = new IdentifiedSpectrum();
IdentifiedPeptide p1 = new IdentifiedPeptide(s1);
p1.Sequence = "B.CDEDF.D";
protein.Peptides.Add(p1);
protein.CalculateCoverage();
Assert.AreEqual(16.67, protein.Coverage, 0.01);
IdentifiedSpectrum s2 = new IdentifiedSpectrum();
IdentifiedPeptide p2 = new IdentifiedPeptide(s2);
p2.Sequence = "F.DSESL.K";
protein.Peptides.Add(p2);
protein.CalculateCoverage();
Assert.AreEqual(33.33, protein.Coverage, 0.01);
IdentifiedSpectrum s3 = new IdentifiedSpectrum();
IdentifiedPeptide p3 = new IdentifiedPeptide(s3);
p3.Sequence = "L.SLGF.G";
protein.Peptides.Add(p3);
protein.CalculateCoverage();
Assert.AreEqual(46.67, protein.Coverage, 0.01);
IdentifiedSpectrum s4 = new IdentifiedSpectrum();
IdentifiedPeptide p4 = new IdentifiedPeptide(s4);
p4.Sequence = "L.SLGFG.D";
protein.Peptides.Add(p4);
protein.CalculateCoverage();
Assert.AreEqual(50.00, protein.Coverage, 0.01);
}
public void TestNoredundant()
{
string header = "\t\"File, Scan(s)\"\tSequence\tMH+\tDiff(MH+)\tCharge\tRank\tScore\tDeltaScore\tExpectValue\tQuery\tIons\tReference\tDIFF_MODIFIED_CANDIDATE\tPI\tMissCleavage\tModification";
IPropertyConverter <IIdentifiedSpectrum> converter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(header, '\t');
Assert.AreEqual(header, converter.Name);
IIdentifiedSpectrum mphit = new IdentifiedSpectrum();
mphit.Query.FileScan.ShortFileName = "AAA,1-2";
IdentifiedPeptide mp1 = new IdentifiedPeptide(mphit);
mp1.Sequence = "AAAAA";
mp1.AddProtein("PROTEIN1");
mp1.AddProtein("PROTEIN2");
IdentifiedPeptide mp2 = new IdentifiedPeptide(mphit);
mp2.Sequence = "BBBBB";
mp2.AddProtein("PROTEIN3");
mphit.TheoreticalMH = 1000.00102;
mphit.ExperimentalMH = 1000.0;
mphit.Query.Charge = 2;
mphit.Rank = 1;
mphit.Score = 100.2;
mphit.DeltaScore = 0.5;
mphit.ExpectValue = 1.1e-2;
mphit.Query.QueryId = 10;
mphit.NumMissedCleavages = 1;
mphit.Modifications = "O18(1)";
string expect = " AAA,1 - 2 AAAAA ! BBBBB 1000.00102 0.00102 2 1 100.2 0.5 1.10E-002 10 0|0 PROTEIN1/PROTEIN2 ! PROTEIN3 0.00 1 O18(1)";
Assert.AreEqual(expect, converter.GetProperty(mphit));
string expectNew = " BBB,2 - 3 BBBBB 1002.00783 -0.00200 3 2 200.2 0.6 1.20E-003 20 0|0 PROTEIN2/PROTEIN4 0.00 2 O18(2)";
converter.SetProperty(mphit, expectNew);
Assert.AreEqual(expectNew, converter.GetProperty(mphit));
}
public void SetUp()
{
s1 = new IdentifiedSpectrum();
s1.Query.FileScan.ShortFileName = "YEAST_0610_G1_SAX_080811_01,11110";
s1.Query.Charge = 2;
s1.Score = 3.0;
s1.AddPeptide(new IdentifiedPeptide(s1)
{
Sequence = "R.#VK*PDR.T"
});
s2 = new IdentifiedSpectrum();
s2.Query.FileScan.ShortFileName = "YEAST_0610_G1_SAX_080811_01,11110";
s2.Query.Charge = 2;
s2.Score = 2.0;
s2.AddPeptide(new IdentifiedPeptide(s2)
{
Sequence = "R.#VK*PDR.T"
});
s3 = new IdentifiedSpectrum();
s3.Score = 1.0;
s3.Query.FileScan.ShortFileName = "YEAST_0610_G1_SAX_080811_01,11110";
s3.Query.Charge = 3;
s3.AddPeptide(new IdentifiedPeptide(s3)
{
Sequence = "R.#VK*PDDEFER.T"
});
s4 = new IdentifiedSpectrum();
s4.Query.FileScan.ShortFileName = "YEAST_0610_G1_SAX_080811_01,11111";
s4.Query.Charge = 3;
s4.Score = 5.0;
s4.AddPeptide(new IdentifiedPeptide(s4)
{
Sequence = "R.#VK*PDDSKEIEFER.T"
});
s5 = new IdentifiedSpectrum();
s5.Query.FileScan.ShortFileName = "YEAST_0610_G1_SAX_080811_01,11111";
s5.Query.Charge = 3;
s5.Score = 4.0;
s5.AddPeptide(new IdentifiedPeptide(s5)
{
Sequence = "R.#VK*PEESKEIEFER.T"
});
s6 = new IdentifiedSpectrum();
s6.Query.FileScan.ShortFileName = "YEAST_0610_G1_SAX_080811_01,11111";
s6.Query.Charge = 2;
s6.Score = 3.0;
s6.AddPeptide(new IdentifiedPeptide(s6)
{
Sequence = "R.#VK*PEESEFER.T"
});
s7 = new IdentifiedSpectrum();
s7.Query.FileScan.ShortFileName = "YEAST_0610_G1_SAX_080811_01,11111";
s7.Query.Charge = 2;
s7.Score = 3.0;
s7.AddPeptide(new IdentifiedPeptide(s7)
{
Sequence = "R.#VKPEESEFER*.T"
});
}
