public void TestBuild()
{
var pep1 = new IdentifiedPeptide(new IdentifiedSpectrum(new SequestFilename("A", 1, 1, 1, ".dta")))
{
Sequence = "A"
};
var pep2 = new IdentifiedPeptide(new IdentifiedSpectrum(new SequestFilename("B", 1, 1, 1, ".dta")))
{
Sequence = "B"
};
var pep3 = new IdentifiedPeptide(new IdentifiedSpectrum(new SequestFilename("C", 1, 1, 1, ".dta")))
{
Sequence = "C"
};
var pep4 = new IdentifiedPeptide(new IdentifiedSpectrum(new SequestFilename("D", 1, 1, 1, ".dta")))
{
Sequence = "D"
};
var pep5 = new IdentifiedPeptide(new IdentifiedSpectrum(new SequestFilename("E", 1, 1, 1, ".dta")))
{
Sequence = "E"
};
var pep6 = new IdentifiedPeptide(new IdentifiedSpectrum(new SequestFilename("F", 1, 1, 1, ".dta")))
{
Sequence = "F"
};
var protein1 = new IdentifiedProtein()
{
Peptides = new IIdentifiedPeptide[] { pep1, pep3, pep5, pep6 }.ToList()
};
var protein2 = new IdentifiedProtein()
{
Peptides = new IIdentifiedPeptide[] { pep2, pep3, pep4 }.ToList()
};
//should be removed from final result since all peptides has been included in protein1 and protein2, even one protein contains both peptides
var protein3 = new IdentifiedProtein()
{
Peptides = new IIdentifiedPeptide[] { pep1, pep2 }.ToList()
};
//should be removed from final result since all peptides has been included in protein1
var protein4 = new IdentifiedProtein()
{
Peptides = new IIdentifiedPeptide[] { pep1, pep5 }.ToList()
};
var actual = new IdentifiedProteinGroupBuilder().Build(new IIdentifiedProtein[] { protein1, protein2, protein3 }.ToList());
Assert.AreEqual(2, actual.Count);
Assert.AreSame(protein1, actual[0][0]);
Assert.AreSame(protein2, actual[1][0]);
}
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));
}
private void AssignPeptideValue(IIdentifiedSpectrum result, Dictionary <string, string> elements, string protein)
{
result.Query.FileScan.Scan = elements["file"];
IIdentifiedPeptide sp = new IdentifiedPeptide(result);
sp.Sequence = elements["sequence"];
sp.AddProtein(protein);
result.TheoreticalMH = MyConvert.ToDouble(elements["mass"]);
result.ExperimentalMH = result.TheoreticalMH - MyConvert.ToDouble(elements["deltamass"]);
result.Query.Charge = int.Parse(elements["charge"]);
result.Score = MyConvert.ToDouble(elements["xcorr"]);
double DeltaScore = MyConvert.ToDouble(elements["deltacn"]);
result.DeltaScore = Math.Min(1.0, DeltaScore);
result.SpScore = MyConvert.ToDouble(elements["sp"]);
result.SpRank = int.Parse(elements["rsp"]);
result.Ions = elements["ions"];
return;
}
