protected override void PrintItem(StreamWriter pw, CalculationItem calculationItem)
{
pw.Write("{0}", calculationItem.Key);
foreach (var s in option.GetClassifiedNames())
{
Count count = calculationItem.Classifications[s];
pw.Write("\t" + count.PeptideCount);
pw.Write("\t" + GetRank(peptideCounts[s], count.PeptideCount));
}
}
public void TestClassifyPeptideHit()
{
List <IIdentifiedSpectrum> spectra = new List <IIdentifiedSpectrum>();
spectra.Add(new IdentifiedSpectrum()
{
Rank = 1
});
spectra.Add(new IdentifiedSpectrum()
{
Rank = 1
});
spectra.Add(new IdentifiedSpectrum()
{
Rank = 2
});
spectra.Add(new IdentifiedSpectrum()
{
Rank = 2
});
new IdentifiedPeptide(spectra[0])
{
Sequence = "SE*Q"
};
new IdentifiedPeptide(spectra[1])
{
Sequence = "SEQ"
};
new IdentifiedPeptide(spectra[2])
{
Sequence = "SEQSEQ"
};
new IdentifiedPeptide(spectra[3])
{
Sequence = "SEQSEQSEQ"
};
CalculationItem item = new CalculationItem()
{
Peptides = spectra.ConvertAll(m => m.Peptide).ToList()
};
item.ClassifyPeptideHit(m => m.Spectrum.Rank.ToString(), new string[] { "1", "2" });
Assert.AreEqual(2, item.Classifications.Count);
Assert.AreEqual(2, item.Classifications["1"].PeptideCount);
Assert.AreEqual(1, item.Classifications["1"].UniquePeptideCount);
Assert.AreEqual(2, item.Classifications["2"].PeptideCount);
Assert.AreEqual(2, item.Classifications["2"].UniquePeptideCount);
}
protected override void PrintItem(StreamWriter pw, CalculationItem calculationItem)
{
IIdentifiedProteinGroup progroup = (IIdentifiedProteinGroup)calculationItem.Key;
pw.Write(StringUtils.Merge(
from p in progroup select parser.GetValue(p.Name),
" ! "));
pw.Write("\t");
pw.Write(StringUtils.Merge(
from p in progroup select p.Description,
" ! "));
PrintClassifiedPeptideCount(pw, calculationItem);
}
public void TestClassifyPeptideHit2()
{
var ir = new SequestResultTextFormat().ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/TestDistributionOption.noredundant");
CalculationItem item = new CalculationItem()
{
Peptides = ir[0][0].GetDistinctPeptides()
};
item.ClassifyPeptideHit(m => "G1");
Assert.AreEqual(1360, item.Classifications["G1"].PeptideCount);
Assert.AreEqual(24, item.Classifications["G1"].UniquePeptideCount);
item.Peptides = ir[1][0].GetDistinctPeptides();
item.ClassifyPeptideHit(m => "G1");
Assert.AreEqual(5, item.Classifications["G1"].PeptideCount);
Assert.AreEqual(1, item.Classifications["G1"].UniquePeptideCount);
}
protected void PrintClassifiedPeptideCount(StreamWriter pw, CalculationItem calculationItem)
{
if (!ExportPeptideCountOnly)
{
foreach (var s in option.GetClassifiedNames())
{
Count count = calculationItem.Classifications[s];
pw.Write("\t" + count.UniquePeptideCount);
pw.Write("\t" + GetRank(uniquePeptideCounts[s], count.UniquePeptideCount));
}
}
foreach (var s in option.GetClassifiedNames())
{
Count count = calculationItem.Classifications[s];
pw.Write("\t" + count.PeptideCount);
if (!ExportPeptideCountOnly)
{
pw.Write("\t" + GetRank(peptideCounts[s], count.PeptideCount));
}
}
}
/// <summary> /// 打印item相关的信息，主要是标识、理论值、实验值、以及分布count数，应该与PrintHeader中定义的标题行一致。 /// </summary> /// <param name="sw"></param> /// <param name="item"></param> protected abstract void PrintItem(StreamWriter sw, CalculationItem item);
