public void TestFilter()
{
var pro1 = new IdentifiedProtein("P1");
pro1.Peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum() { Charge = 1 }));
pro1.Peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum() { Charge = 2 }));
var pro2 = new IdentifiedProtein("P2");
pro2.Peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum() { Charge = 3 }));
var g1 = new IdentifiedProteinGroup();
g1.Add(pro1);
var g2 = new IdentifiedProteinGroup();
g2.Add(pro2);
IdentifiedResult ir = new IdentifiedResult();
ir.Add(g1);
ir.Add(g2);
Assert.AreEqual(2, ir.Count);
Assert.AreEqual(3, ir.GetSpectra().Count);
ir.Filter(m => { return m.Spectrum.Query.Charge > 1; });
Assert.AreEqual(2, ir.Count);
Assert.AreEqual(2, ir.GetSpectra().Count);
ir.GetSpectra().All(m => { return m.Charge > 1; });
ir.Filter(m => { return m.Spectrum.Query.Charge > 2; });
Assert.AreEqual(1, ir.Count);
Assert.AreEqual(1, ir.GetSpectra().Count);
ir.GetSpectra().All(m => { return m.Charge > 2; });
Assert.AreEqual("P2", ir[0][0].Name);
}
public void Run()
{
IdentifiedProteinGroupContaminationDescriptionFilter filter = new IdentifiedProteinGroupContaminationDescriptionFilter("KERATIN");
IdentifiedProteinGroup group = new IdentifiedProteinGroup();
group.Add(new IdentifiedProtein("P1")
{
Description = "P1 Keratin"
});
Assert.IsTrue(filter.Accept(group));
}
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 TestProcess()
{
IIdentifiedProteinGroup group = new IdentifiedProteinGroup();
group.Add(new IdentifiedProtein("BBBCCC"));
group.Add(new IdentifiedProtein("AAABBB"));
IIdentifiedProteinGroup finalGroup;
///两者都有，两个都保留
finalGroup = new ProteinNameProcessor(new string[]{"BBB"}).Process(group);
Assert.AreEqual(2, finalGroup.Count);
///两者都没有，两个都保留
finalGroup = new ProteinNameProcessor(new string[] { "DDD" }).Process(group);
Assert.AreEqual(2, finalGroup.Count);
///只有一个有，保留这一个
finalGroup = new ProteinNameProcessor(new string[] { "AAA" }).Process(group);
Assert.AreEqual(1, finalGroup.Count);
Assert.AreEqual("AAABBB", finalGroup[0].Name);
}
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 TestGetAnnotationKeys()
{
string key1 = "TEST1";
string key2 = "TEST2";
var mph1 = new IdentifiedSpectrum();
mph1.Annotations.Add(key1, null);
mph1.Query.FileScan.Experimental = "EXP1";
new IdentifiedPeptide(mph1);
var mph2 = new IdentifiedSpectrum();
mph2.Annotations.Add(key2, null);
mph2.Query.FileScan.Experimental = "EXP2";
new IdentifiedPeptide(mph2);
mph1.Peptide.Sequence = "SEQ1";
mph2.Peptide.Sequence = "SEQ2";
var protein = new IdentifiedProtein();
protein.Peptides.Add(mph1.Peptide);
protein.Peptides.Add(mph2.Peptide);
var mpg = new IdentifiedProteinGroup();
mpg.Add(protein);
var mr = new MascotResult();
mr.Add(mpg);
List<string> annotationKeys = AnnotationUtils.GetAnnotationKeys(mr.GetSpectra());
Assert.AreEqual(2, annotationKeys.Count);
Assert.IsTrue(annotationKeys.Contains(key1));
Assert.IsTrue(annotationKeys.Contains(key2));
}
