public void TestDtaselect()
{
string header = "Locus Sequence Count Spectrum Count Sequence Coverage Length MolWt pI Validation Status Descriptive Name";
IPropertyConverter <IIdentifiedProtein> converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(header, '\t');
Assert.AreEqual(header, converter.Name);
string line = "YDR050C 495 495 81.10% 249 26795.41 5.74 U YDR050C TPI1 SGDID:S000002457, Chr IV from 556470-555724, reverse complement, Verified ORF, \"Triose phosphate isomerase, abundant glycolytic enzyme; mRNA half-life is regulated by iron availability; transcription is controlled by activators Reb1p, Gcr1p, and Rap1p through binding sites in the 5' non-coding region\"";
IIdentifiedProtein protein = new IdentifiedProtein();
converter.SetProperty(protein, line);
Assert.AreEqual("YDR050C", protein.Name);
Assert.AreEqual("TPI1 SGDID:S000002457, Chr IV from 556470-555724, reverse complement, Verified ORF, \"Triose phosphate isomerase, abundant glycolytic enzyme; mRNA half-life is regulated by iron availability; transcription is controlled by activators Reb1p, Gcr1p, and Rap1p through binding sites in the 5' non-coding region\"", protein.Description);
Assert.AreEqual(495, protein.UniquePeptideCount);
Assert.AreEqual(81.1, protein.Coverage);
Assert.AreEqual(26795.41, protein.MolecularWeight);
Assert.AreEqual(5.74, protein.IsoelectricPoint);
for (int i = 0; i < 495; i++)
{
protein.Peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum()));
}
Assert.AreEqual(line, converter.GetProperty(protein));
}
public void TestNoredundant()
{
string header = " Reference PepCount UniquePepCount CoverPercent MW PI IdentifiedName";
IPropertyConverter <IIdentifiedProtein> converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(header, '\t');
Assert.AreEqual(header, converter.Name);
string line = "\tIPI:IPI00784154.1|SWISS-PROT:P10809|TREMBL:B2R5M6;Q53QD5;Q53SE2;Q96RI4;Q9UCR6|ENSEMBL:ENSP00000340019;ENSP00000373620|REFSEQ:NP_002147;NP_955472|H-INV:HIT000031088 Tax_Id=9606 Gene_Symbol=HSPD1 60 kDa heat shock protein, mitochondrial 84 19 43.46% 61054.43 5.70 IPI:IPI00784154.1|SWISS-PROT:P10809|TREMBL:B2R5M6;Q53QD5;Q53SE2;Q96RI4;Q9UCR6|ENSEMBL:ENSP00000340019;ENSP00000373620|REFSEQ:NP_002147;NP_955472|H-INV:HIT000031088 Tax_Id=9606 Gene_Symbol=HSPD1 60 kDa heat shock protein, mitochondrial";
IIdentifiedProtein protein = new IdentifiedProtein();
converter.SetProperty(protein, line);
Assert.AreEqual("IPI:IPI00784154.1|SWISS-PROT:P10809|TREMBL:B2R5M6;Q53QD5;Q53SE2;Q96RI4;Q9UCR6|ENSEMBL:ENSP00000340019;ENSP00000373620|REFSEQ:NP_002147;NP_955472|H-INV:HIT000031088", protein.Name);
Assert.AreEqual("Tax_Id=9606 Gene_Symbol=HSPD1 60 kDa heat shock protein, mitochondrial", protein.Description);
Assert.AreEqual(19, protein.UniquePeptideCount);
Assert.AreEqual(43.46, protein.Coverage);
Assert.AreEqual(61054.43, protein.MolecularWeight);
Assert.AreEqual(5.7, protein.IsoelectricPoint);
for (int i = 0; i < 84; i++)
{
protein.Peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum()));
}
Assert.AreEqual(line, converter.GetProperty(protein));
}
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 override string GetProperty(T t)
{
return(baseConverter.GetProperty(t));
}
