private static void TestIsolationWindowMapper(AbstractIsoWindowMapper isoMapper, MsDataFileImpl file, double width)
{
// Check the first five spectra in the file
for (int checkIndex = 0; checkIndex < 5; ++checkIndex)
{
var spectrum = file.GetSpectrum(checkIndex);
var precursors = spectrum.Precursors;
List <int> isoIndices = new List <int>();
// Make sure that each precursor read from the file is included in the isolation
// window mapper
foreach (var precursor in precursors)
{
int index;
Assert.IsTrue(precursor.IsolationMz.HasValue);
Assert.IsTrue(isoMapper.TryGetWindowIndex(precursor.IsolationMz.Value, out index));
isoIndices.Add(index);
}
int[] isoIndicesFromMapper;
int[] overlapIndicesFromMapper;
double[] mask = new double[isoMapper.NumWindows];
// Make sure the isolation windows called from GetWindowMask match those
// extracted from the spectrum manually above using TryGetWindowIndex
isoMapper.GetWindowMask(spectrum, out isoIndicesFromMapper, out overlapIndicesFromMapper, ref mask);
Assert.AreEqual(isoIndices.Count, isoIndicesFromMapper.Length);
foreach (int index in isoIndicesFromMapper)
{
Assert.IsTrue(isoIndices.Contains(index));
}
// Make sure the overlapIndicesFromMapper matches the mask
for (int i = 0; i < mask.Length; ++i)
{
if (mask[i] < 0.5)
{
Assert.AreEqual(0.0, mask[i]);
}
else
{
Assert.AreEqual(1.0, mask[i]);
Assert.IsTrue(overlapIndicesFromMapper.Contains(i));
}
}
}
var testMzs = new[] { 553.49, 623.7, 859, 658.55, 768.7, 621.52 };
// For each test m/z, get the matching isolation window from isoMapper and
// make sure the m/z does indeed fall within the window
foreach (var checkMz in testMzs)
{
int windowIndex;
Assert.IsTrue(isoMapper.TryGetWindowFromMz(checkMz, out windowIndex));
var matchWindowCenterMz = isoMapper.GetPrecursor(windowIndex);
Assert.IsTrue(matchWindowCenterMz.IsolationMz.HasValue);
// Check that mz is within window (width/2 )
Assert.IsTrue(Math.Abs(matchWindowCenterMz.IsolationMz.Value - checkMz) < width / 2);
}
// Test out of range precursors
int dummyIndex;
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(315.25, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(1005.2, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
}
private static void TestIsolationWindowMapper(AbstractIsoWindowMapper isoMapper, MsDataFileImpl file, double width)
{
// Check the first five spectra in the file
for (int checkIndex = 0 ; checkIndex < 5; ++checkIndex)
{
var spectrum = file.GetSpectrum(checkIndex);
var precursors = spectrum.Precursors;
List<int> isoIndices = new List<int>();
// Make sure that each precursor read from the file is included in the isolation
// window mapper
foreach (var precursor in precursors)
{
int index;
Assert.IsTrue(precursor.IsolationMz.HasValue);
Assert.IsTrue(isoMapper.TryGetWindowIndex(precursor.IsolationMz.Value, out index));
isoIndices.Add(index);
}
int[] isoIndicesFromMapper;
int[] overlapIndicesFromMapper;
double[] mask = new double[isoMapper.NumWindows];
// Make sure the isolation windows called from GetWindowMask match those
// extracted from the spectrum manually above using TryGetWindowIndex
isoMapper.GetWindowMask(spectrum, out isoIndicesFromMapper, out overlapIndicesFromMapper, ref mask);
Assert.AreEqual(isoIndices.Count,isoIndicesFromMapper.Length);
foreach (int index in isoIndicesFromMapper)
{
Assert.IsTrue(isoIndices.Contains(index));
}
// Make sure the overlapIndicesFromMapper matches the mask
for (int i = 0; i < mask.Length; ++i)
{
if (mask[i] < 0.5)
Assert.AreEqual(0.0, mask[i]);
else
{
Assert.AreEqual(1.0, mask[i]);
Assert.IsTrue(overlapIndicesFromMapper.Contains(i));
}
}
}
var testMzs = new[] {553.49, 623.7, 859, 658.55, 768.7, 621.52};
// For each test m/z, get the matching isolation window from isoMapper and
// make sure the m/z does indeed fall within the window
foreach (var checkMz in testMzs)
{
int windowIndex;
Assert.IsTrue(isoMapper.TryGetWindowFromMz(checkMz, out windowIndex));
var matchWindowCenterMz = isoMapper.GetPrecursor(windowIndex);
Assert.IsTrue(matchWindowCenterMz.IsolationMz.HasValue);
// Check that mz is within window (width/2 )
Assert.IsTrue(Math.Abs(matchWindowCenterMz.IsolationMz.Value - checkMz) < width/2);
}
// Test out of range precursors
int dummyIndex;
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(315.25, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(1005.2, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
}
