public ITraqResultFileDistiller(IITraqRawReader itraqReader, int minPeakCount, IsobaricType plexType, string isotopeImpurityFile, double precursorPPM)
{
this.itraqReader = itraqReader;
this.minPeakCount = minPeakCount;
this.calc = new IsobaricImpurityCorrectionCalculator(plexType, isotopeImpurityFile);
this.precursorPPM = precursorPPM;
}
public void TestCorrectPlex8()
{
var calc = new IsobaricImpurityCorrectionCalculator(IsobaricType.PLEX8, @TestContext.CurrentContext.TestDirectory + "/../../../data//itraq-8plex.csv");
var b = new List <double>();
var m = calc.CloneTable();
for (int i = 0; i < m[0].Length; i++)
{
b.Add((from mm in m select mm[i]).Sum());
}
var bb = b.ToArray();
double[] x = calc.Correct(bb);
foreach (var v in x)
{
Assert.AreEqual(1, v, 0.001);
}
//repeat again to ensure that the matrix (a) in calc has not been changed.
bb = b.ToArray();
x = calc.Correct(bb);
foreach (var v in x)
{
Assert.AreEqual(1, v, 0.001);
}
}
public void TestParsePlex8()
{
double[][] a = IsobaricImpurityCorrectionCalculator.ParseTable(IsobaricType.PLEX8, @TestContext.CurrentContext.TestDirectory + "/../../../data//itraq-8plex.csv");
// OutputArray(a);
double[][] expect = new double[][] {
new double[] { 0.9287, 0.0689, 0.0024, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000 },
new double[] { 0.0094, 0.9300, 0.0590, 0.0016, 0.0000, 0.0000, 0.0000, 0.0000 },
new double[] { 0.0000, 0.0188, 0.9312, 0.0490, 0.0010, 0.0000, 0.0000, 0.0000 },
new double[] { 0.0000, 0.0000, 0.0282, 0.9321, 0.0390, 0.0007, 0.0000, 0.0000 },
new double[] { 0.0000, 0.0000, 0.0006, 0.0377, 0.9329, 0.0288, 0.0000, 0.0000 },
new double[] { 0.0000, 0.0000, 0.0000, 0.0009, 0.0471, 0.9329, 0.0191, 0.0000 },
new double[] { 0.0000, 0.0000, 0.0000, 0.0000, 0.0014, 0.0566, 0.9333, 0.0000 },
new double[] { 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0027, 0.9211 }
};
for (int i = 0; i < a.Length; i++)
{
for (int j = 0; j < a[i].Length; j++)
{
Assert.AreEqual(a[i][j], expect[i][j], 0.0001);
}
}
}
public void TestCorrectPlex4()
{
var calc = new IsobaricImpurityCorrectionCalculator(IsobaricType.PLEX4, @TestContext.CurrentContext.TestDirectory + "/../../../data//itraq-4plex.csv");
double[] b = new double[] { 0.949, 1.013, 1.022, 0.969 };
double[] x = calc.Correct(b);
foreach (var v in x)
{
Assert.AreEqual(1, v, 0.001);
}
//repeat again to ensure that the matrix (a) in calc has not been changed.
b = new double[] { 0.949, 1.013, 1.022, 0.969 };
x = calc.Correct(b);
foreach (var v in x)
{
Assert.AreEqual(1, v, 0.001);
}
}
public void TestParsePlex4()
{
double[][] a = IsobaricImpurityCorrectionCalculator.ParseTable(IsobaricType.PLEX4, @TestContext.CurrentContext.TestDirectory + "/../../../data//itraq-4plex.csv");
//OutputArray(a);
double[][] expect = new double[][] {
new double[] { 0.9290, 0.0590, 0.0020, 0.0000 },
new double[] { 0.0200, 0.9230, 0.0560, 0.0010 },
new double[] { 0.0000, 0.0300, 0.9240, 0.0450 },
new double[] { 0.0000, 0.0010, 0.0400, 0.9230 }
};
for (int i = 0; i < a.Length; i++)
{
for (int j = 0; j < a[i].Length; j++)
{
Assert.AreEqual(a[i][j], expect[i][j], 0.0001);
}
}
}
public void TestParseTMT6()
{
double[][] a = IsobaricImpurityCorrectionCalculator.ParseTable(IsobaricType.TMT6, @TestContext.CurrentContext.TestDirectory + "/../../../data//TMT-6plex.csv");
//OutputArray(a);
double[][] expect = new double[][] {
new double[] { 0.9232, 0.0768, 0.0000, 0.0000, 0.0000, 0.0000 },
new double[] { 0.0000, 0.9342, 0.0658, 0.0000, 0.0000, 0.0000 },
new double[] { 0.0000, 0.0000, 0.9462, 0.0538, 0.0000, 0.0000 },
new double[] { 0.0000, 0.0000, 0.0140, 0.9406, 0.0454, 0.0000 },
new double[] { 0.0000, 0.0000, 0.0000, 0.0000, 0.9656, 0.0344 },
new double[] { 0.0000, 0.0000, 0.0000, 0.0000, 0.0167, 0.9454 }
};
for (int i = 0; i < a.Length; i++)
{
for (int j = 0; j < a[i].Length; j++)
{
Assert.AreEqual(a[i][j], expect[i][j], 0.0001);
}
}
}
