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));
}
private void InitializeProteinFormat(IIdentifiedResult identifiedResult, string oldProteinHeader)
{
var proteins = identifiedResult.GetProteins();
List <string> proAnnotations = AnnotationUtils.GetAnnotationKeys(proteins);
string newProteinHeader = StringUtils.GetMergedHeader(oldProteinHeader, proAnnotations, '\t');
ProteinFormat = new LineFormat <IIdentifiedProtein>(IdentifiedProteinPropertyConverterFactory.GetInstance(), newProteinHeader, GetEngineName(), proteins);
}
public IdentifiedProteinTextWriter(string proteinHeader, IEnumerable <IIdentifiedProtein> proteins)
{
this._proteins = proteins;
this._annotationKeys = AnnotationUtils.GetAnnotationKeys(this._proteins);
var sb = new StringBuilder();
sb.Append(proteinHeader);
foreach (string key in this._annotationKeys)
{
sb.Append("\t" + key);
}
this.converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(sb.ToString(), '\t');
}
public void Reset()
{
br.DiscardBufferedData();
br.BaseStream.Seek(0, SeekOrigin.Begin);
lastLine = br.ReadLine();
proteinFormat = new LineFormat <IIdentifiedProtein>(IdentifiedProteinPropertyConverterFactory.GetInstance(), lastLine);
lastLine = br.ReadLine();
peptideFormat = new LineFormat <IIdentifiedSpectrum>(IdentifiedSpectrumPropertyConverterFactory.GetInstance(), lastLine);
while ((lastLine = br.ReadLine()) != null)
{
if (lastLine.StartsWith("$"))
{
break;
}
}
}
public ProteinLineFormat(string headers, string engine)
: base(IdentifiedProteinPropertyConverterFactory.GetInstance(), headers, engine)
{
}
public IdentifiedProteinTextWriter(string proteinHeader)
{
this.converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(proteinHeader, '\t');
}
public static IdentifiedProteinPropertyConverterFactory GetInstance()
{
IdentifiedProteinPropertyConverterFactory result = new IdentifiedProteinPropertyConverterFactory();
IPropertyConverter <IIdentifiedProtein> nameConverter = new IdentifiedProteinNameConverter <IIdentifiedProtein>();
result.RegisterConverter(nameConverter);
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(nameConverter, "Locus"));
IPropertyConverter <IIdentifiedProtein> despConverter = new IdentifiedProteinDescriptionConverter <IIdentifiedProtein>();
result.RegisterConverter(despConverter);
IPropertyConverter <IIdentifiedProtein> refConverter = new IdentifiedProteinReferenceConverter <IIdentifiedProtein>();
result.RegisterConverter(refConverter);
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(refConverter, "Descriptive Name"));
IPropertyConverter <IIdentifiedProtein> massConverter = new IdentifiedProteinMassConverter <IIdentifiedProtein>();
result.RegisterConverter(massConverter);
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(massConverter, "MW"));
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(massConverter, "MolWt"));
result.RegisterConverter(new MascotProteinTotalScoreConverter <IIdentifiedProtein>());
IPropertyConverter <IIdentifiedProtein> uniqueConverter = new IdentifiedProteinUniquePeptideCountConverter <IIdentifiedProtein>();
result.RegisterConverter(uniqueConverter);
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(uniqueConverter, "UniquePepCount"));
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(uniqueConverter, "Sequence Count"));
IPropertyConverter <IIdentifiedProtein> spectrumConverter = new IdentifiedProteinSpectrumCountConverter <IIdentifiedProtein>();
result.RegisterConverter(spectrumConverter);
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(spectrumConverter, "Spectrum Count"));
result.RegisterConverter(new AnnotationLinearRegressionRatioResult_RatioConverter <IIdentifiedProtein>("LR_Ratio"));
result.RegisterConverter(new AnnotationLinearRegressionRatioResult_RSquareConverter <IIdentifiedProtein>("LR_Ratio", "LR_RSquare"));
result.RegisterConverter(new AnnotationLinearRegressionRatioResult_FCalcConverter <IIdentifiedProtein>("LR_Ratio", "LR_FCalc"));
result.RegisterConverter(new AnnotationLinearRegressionRatioResult_FProbabilityConverter <IIdentifiedProtein>("LR_Ratio", "LR_FProb"));
IPropertyConverter <IIdentifiedProtein> coverageConverter = new IdentifiedProteinCoverageConverter <IIdentifiedProtein>();
result.RegisterConverter(coverageConverter);
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(coverageConverter, "Sequence Coverage"));
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(coverageConverter, "CoverPercent"));
IPropertyConverter <IIdentifiedProtein> piConverter = new IdentifiedProteinIsoelectricPointConverterter <IIdentifiedProtein>();
result.RegisterConverter(piConverter);
result.RegisterConverter(new PropertyAliasConverter <IIdentifiedProtein>(piConverter, "pI"));
result.RegisterConverter(new AnnotationConverter <IIdentifiedProtein>("Length", "1"));
result.RegisterConverter(new AnnotationConverter <IIdentifiedProtein>("Validation Status", "U"));
result.RegisterConverter(new QuantificationItemRatioConverter <IIdentifiedProtein>());
result._ignoreKey.Add("S_FILE");
result._ignoreKey.Add("S_SCANS");
result.RegisterConverter(new SilacProteinQuantificationResultConverter2 <IIdentifiedProtein>());
result.RegisterConverter(new ITraqQuantificationResultConverter <IIdentifiedProtein>());
result.RegisterConverter(new IdentifiedProteinDecoyConverter <IIdentifiedProtein>());
return(result);
}
