public void TestDtaselect()
{
string header = "Unique FileName Score DeltCN M+H+ CalcM+H+ TotalIntensity SpRank SpScore IonProportion Redundancy Sequence";
IPropertyConverter <IIdentifiedSpectrum> converter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(header, '\t');
Assert.AreEqual(header, converter.Name);
}
public static IdentifiedSpectrumPropertyConverterFactory GetInstance()
{
if (factory == null)
{
factory = new IdentifiedSpectrumPropertyConverterFactory();
}
return(factory);
}
private void InitializePeptideFormat(IIdentifiedResult identifiedResult, string oldPeptideHeader)
{
var spectra = identifiedResult.GetSpectra();
List <string> pepAnnotations = AnnotationUtils.GetAnnotationKeys(spectra);
string newPeptideHeader = StringUtils.GetMergedHeader(oldPeptideHeader, pepAnnotations, '\t');
PeptideFormat = new LineFormat <IIdentifiedSpectrum>(IdentifiedSpectrumPropertyConverterFactory.GetInstance(), newPeptideHeader, GetEngineName(), spectra);
}
public void TestDtaselectConverter()
{
IPropertyConverter <IIdentifiedSpectrum> converter;
converter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().FindConverter("Sequence");
Assert.AreEqual(converter.GetType(), new IdentifiedSpectrumSequenceConverter <IIdentifiedSpectrum>().GetType());
converter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().FindConverter("Sequence", "Dtaselect");
Assert.AreEqual(converter.GetType(), new IdentifiedSpectrumSequenceConverterDtaselect <IIdentifiedSpectrum>().GetType());
converter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().FindConverter("\"File, Scan(s)\"");
Assert.AreEqual(converter.GetType(), new IdentifiedSpectrumFileScanConverter <IIdentifiedSpectrum>().GetType());
converter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().FindConverter("FileName");
Assert.AreEqual(converter.GetType(), new IdentifiedSpectrumFileScanConverterDtaselect <IIdentifiedSpectrum>().GetType());
converter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().FindConverter("FileName", "Dtaselect");
Assert.AreEqual(converter.GetType(), new IdentifiedSpectrumFileScanConverterDtaselect <IIdentifiedSpectrum>().GetType());
}
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 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 PeptideLineFormat(string headers, string engine, List <IIdentifiedSpectrum> items)
: base(IdentifiedSpectrumPropertyConverterFactory.GetInstance(), headers, engine, items)
{
}
public PeptideLineFormat(string headers)
: base(IdentifiedSpectrumPropertyConverterFactory.GetInstance(), headers)
{
}