private void CheckPlexType(IsobaricType plexType, string expectHeader, string expectValue)
{
var ann = new IdentifiedSpectrum();
var pqr = new IsobaricItem()
{
PlexType = plexType,
Valid = true,
ValidProbability = 0.0005
};
var refItems = plexType.GetDefinition().Items;
foreach (var item in refItems)
{
pqr[item.Index] = item.Mass;
}
ann.SetIsobaricItem(pqr);
//从实例构建converter
var converter = new ITraqItemPlexConverter <IAnnotation>();
List <IPropertyConverter <IAnnotation> > converters = new List <IPropertyConverter <IAnnotation> >();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter <IAnnotation> finalConverter = new CompositePropertyConverter <IAnnotation>(converters, ',');
if (exportToConsole)
{
Console.WriteLine(finalConverter.Name);
}
Assert.AreEqual(expectHeader, finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
if (exportToConsole)
{
Console.WriteLine(line1);
}
Assert.AreEqual(expectValue, line1);
var protein2 = new IdentifiedSpectrum();
//从factory根据header构建converter
var finalC = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
public void TestReadWrite()
{
var ann = new IdentifiedProtein();
var pqr = new ProteinQuantificationResult();
pqr.Items["D1"] = new QuantificationItem()
{
Enabled = true,
Ratio = 1.5,
SampleIntensity = 150,
ReferenceIntensity = 100,
Correlation = 0.9,
ScanCount = 55,
Filename = "test1.silac"
};
pqr.Items["D2"] = new QuantificationItem()
{
Enabled = false,
Ratio = 3,
SampleIntensity = 250,
ReferenceIntensity = 200,
Correlation = 0.8,
ScanCount = 77,
Filename = "test2.silac"
};
ann.Annotations[SilacQuantificationConstants.SILAC_KEY] = pqr;
var converter = new SilacProteinQuantificationResultConverter2 <IAnnotation>();
List <IPropertyConverter <IAnnotation> > converters = new List <IPropertyConverter <IAnnotation> >();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter <IAnnotation> finalConverter = new CompositePropertyConverter <IAnnotation>(converters, ',');
Assert.AreEqual("S_COUNT,SE_D1,SR_D1,SRC_D1,SSI_D1,SRI_D1,SE_D2,SR_D2,SRC_D2,SSI_D2,SRI_D2", finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
Assert.AreEqual("2,True,1.5000,0.9000,150.0,100.0,False,3.0000,0.8000,250.0,200.0", line1);
var protein2 = new IdentifiedProtein();
var finalC = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
public void TestReadWrite()
{
var ann = new IdentifiedProtein();
var pqr = new ProteinQuantificationResult();
pqr.Items["D1"] = new QuantificationItem()
{
Enabled = true,
Ratio = 1.5,
SampleIntensity = 150,
ReferenceIntensity = 100,
Correlation = 0.9,
ScanCount = 55,
Filename = "test1.silac"
};
pqr.Items["D2"] = new QuantificationItem()
{
Enabled = false,
Ratio = 3,
SampleIntensity = 250,
ReferenceIntensity = 200,
Correlation = 0.8,
ScanCount = 77,
Filename = "test2.silac"
};
ann.Annotations[SilacQuantificationConstants.SILAC_KEY] = pqr;
var converter = new SilacProteinQuantificationResultConverter2<IAnnotation>();
List<IPropertyConverter<IAnnotation>> converters = new List<IPropertyConverter<IAnnotation>>();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter<IAnnotation> finalConverter = new CompositePropertyConverter<IAnnotation>(converters, ',');
Assert.AreEqual("S_COUNT,SE_D1,SR_D1,SRC_D1,SSI_D1,SRI_D1,SE_D2,SR_D2,SRC_D2,SSI_D2,SRI_D2", finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
Assert.AreEqual("2,True,1.5000,0.9000,150.0,100.0,False,3.0000,0.8000,250.0,200.0", line1);
var protein2 = new IdentifiedProtein();
var finalC = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
private void CheckPlexType(IsobaricType plexType, string expectHeader, string expectValue)
{
var ann = new IdentifiedSpectrum();
var pqr = new IsobaricItem()
{
PlexType = plexType,
Valid = true,
ValidProbability = 0.0005
};
var refItems = plexType.GetDefinition().Items;
foreach (var item in refItems)
{
pqr[item.Index] = item.Mass;
}
ann.SetIsobaricItem(pqr);
//从实例构建converter
var converter = new ITraqItemPlexConverter<IAnnotation>();
List<IPropertyConverter<IAnnotation>> converters = new List<IPropertyConverter<IAnnotation>>();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter<IAnnotation> finalConverter = new CompositePropertyConverter<IAnnotation>(converters, ',');
if (exportToConsole)
{
Console.WriteLine(finalConverter.Name);
}
Assert.AreEqual(expectHeader, finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
if (exportToConsole)
{
Console.WriteLine(line1);
}
Assert.AreEqual(expectValue, line1);
var protein2 = new IdentifiedSpectrum();
//从factory根据header构建converter
var finalC = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
public void TestReadWrite()
{
var ann = new IdentifiedProtein();
var pqr = new ITraqQuantificationResult();
pqr.DatasetMap["D1"] = new ITraqQuantificationDatasetItem()
{
DatasetName = "D1"
};
pqr.DatasetMap["D1"].RatioMap["R114/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R114/REF",
Ratio = 1.5
};
pqr.DatasetMap["D1"].RatioMap["R115/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R115/REF",
Ratio = 1.8
};
pqr.DatasetMap["D2"] = new ITraqQuantificationDatasetItem()
{
DatasetName = "D2"
};
pqr.DatasetMap["D2"].RatioMap["R116/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R116/REF",
Ratio = 2.5
};
pqr.DatasetMap["D2"].RatioMap["R117/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R117/REF",
Ratio = 3.8
};
ann.Annotations[ITraqConsts.ITRAQ_KEY] = pqr;
var converter = new ITraqQuantificationResultConverter <IAnnotation>();
List <IPropertyConverter <IAnnotation> > converters = new List <IPropertyConverter <IAnnotation> >();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter <IAnnotation> finalConverter = new CompositePropertyConverter <IAnnotation>(converters, ',');
if (exportToConsole)
{
Console.WriteLine(finalConverter.Name);
}
Assert.AreEqual("ITRAQ_COUNT,IR_D1_R114/REF,IR_D1_R115/REF,IR_D2_R116/REF,IR_D2_R117/REF", finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
if (exportToConsole)
{
Console.WriteLine(line1);
}
Assert.AreEqual("2,1.5000,1.8000,2.5000,3.8000", line1);
var protein2 = new IdentifiedProtein();
var finalC = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
public void TestReadWrite()
{
var ann = new IdentifiedProtein();
var pqr = new ITraqQuantificationResult();
pqr.DatasetMap["D1"] = new ITraqQuantificationDatasetItem()
{
DatasetName = "D1"
};
pqr.DatasetMap["D1"].RatioMap["R114/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R114/REF",
Ratio = 1.5
};
pqr.DatasetMap["D1"].RatioMap["R115/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R115/REF",
Ratio = 1.8
};
pqr.DatasetMap["D2"] = new ITraqQuantificationDatasetItem()
{
DatasetName = "D2"
};
pqr.DatasetMap["D2"].RatioMap["R116/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R116/REF",
Ratio = 2.5
};
pqr.DatasetMap["D2"].RatioMap["R117/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R117/REF",
Ratio = 3.8
};
ann.Annotations[ITraqConsts.ITRAQ_KEY] = pqr;
var converter = new ITraqQuantificationResultConverter<IAnnotation>();
List<IPropertyConverter<IAnnotation>> converters = new List<IPropertyConverter<IAnnotation>>();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter<IAnnotation> finalConverter = new CompositePropertyConverter<IAnnotation>(converters, ',');
if (exportToConsole)
{
Console.WriteLine(finalConverter.Name);
}
Assert.AreEqual("ITRAQ_COUNT,IR_D1_R114/REF,IR_D1_R115/REF,IR_D2_R116/REF,IR_D2_R117/REF", finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
if (exportToConsole)
{
Console.WriteLine(line1);
}
Assert.AreEqual("2,1.5000,1.8000,2.5000,3.8000", line1);
var protein2 = new IdentifiedProtein();
var finalC = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
