/// Fill up transition group with paired Transitions and Chromatograms
void getTransitionGroup(OpenSwath::SpectrumAccessPtr input, MRMTransitionGroupType& transition_group, String id)
{
transition_group.setTransitionGroupID(id);
// Go through all transitions
for (Size i = 0; i < assay_map[id].size(); i++)
{
// Check first whether we have a mapping (e.g. see -force option)
const TransitionType* transition = assay_map[id][i];
if (chromatogram_map.find(transition->getNativeID()) == chromatogram_map.end())
{
LOG_DEBUG << "Found no matching chromatogram for id " << transition->getNativeID() << std::endl;
continue;
}
OpenSwath::ChromatogramPtr cptr = input->getChromatogramById(chromatogram_map[transition->getNativeID()]);
MSChromatogram chromatogram;
OpenSwathDataAccessHelper::convertToOpenMSChromatogram(cptr, chromatogram);
chromatogram.setMetaValue("product_mz", transition->getProductMZ());
chromatogram.setMetaValue("precursor_mz", transition->getPrecursorMZ());
chromatogram.setNativeID(transition->getNativeID());
// Now add the transition and the chromatogram to the group
transition_group.addTransition(*transition, transition->getNativeID());
transition_group.addChromatogram(chromatogram, chromatogram.getNativeID());
}
}
void setup_transition_group(MRMTransitionGroupType & transition_group)
{
// this is a simulated SRM experiment where the two traces are not sampled at
// the exact same time points, thus a resampling is necessary before applying
// the algorithm.
static const double rtdata_1[] = {1474.34, 1477.11, 1479.88, 1482.64, 1485.41, 1488.19, 1490.95, 1493.72, 1496.48, 1499.25, 1502.03, 1504.8 , 1507.56, 1510.33, 1513.09, 1515.87, 1518.64, 1521.42};
static const double rtdata_2[] = {1473.55, 1476.31, 1479.08, 1481.84, 1484.61, 1487.39, 1490.15, 1492.92, 1495.69, 1498.45, 1501.23, 1504 , 1506.76, 1509.53, 1512.29, 1515.07, 1517.84, 1520.62};
static const double intdata_1[] = {3.26958, 3.74189, 3.31075, 86.1901, 3.47528, 387.864, 13281 , 6375.84, 39852.6, 2.66726, 612.747, 3.34313, 793.12 , 3.29156, 4.00586, 4.1591 , 3.23035, 3.90591};
static const double intdata_2[] = {3.44054 , 2142.31 , 3.58763 , 3076.97 , 6663.55 , 45681 , 157694 , 122844 , 86034.7 , 85391.1 , 15992.8 , 2293.94 , 6934.85 , 2735.18 , 459.413 , 3.93863 , 3.36564 , 3.44005};
{
RichPeakChromatogram chromatogram;
for (int k = 0; k < 18; k++)
{
ChromatogramPeak peak;
peak.setMZ(rtdata_1[k]);
peak.setIntensity(intdata_1[k]);
chromatogram.push_back(peak);
}
chromatogram.setMetaValue("product_mz", 618.31);
chromatogram.setNativeID("1");
transition_group.addChromatogram(chromatogram, chromatogram.getNativeID());
}
{
RichPeakChromatogram chromatogram;
for (int k = 0; k < 18; k++)
{
ChromatogramPeak peak;
peak.setMZ(rtdata_2[k]);
peak.setIntensity(intdata_2[k]);
chromatogram.push_back(peak);
}
chromatogram.setMetaValue("product_mz", 619.31);
chromatogram.setNativeID("2");
transition_group.addChromatogram(chromatogram, chromatogram.getNativeID());
}
}
START_SECTION(MRMTransitionGroupPicker())
{
ptr = new MRMTransitionGroupPicker();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(~MRMTransitionGroupPicker())
{
delete ptr;
}
END_SECTION
START_SECTION((template < typename SpectrumT, typename TransitionT > void pickTransitionGroup(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group)))
{
MRMTransitionGroupType transition_group;
setup_transition_group(transition_group);
MRMTransitionGroupPicker trgroup_picker;
trgroup_picker.pickTransitionGroup(transition_group);
TEST_EQUAL(transition_group.getFeatures().size(), 1)
MRMFeature mrmfeature = transition_group.getFeatures()[0];
TEST_REAL_SIMILAR(mrmfeature.getRT(), 1492.83060);
TEST_REAL_SIMILAR( mrmfeature.getMetaValue("leftWidth"), 1481.84);
TEST_REAL_SIMILAR( mrmfeature.getMetaValue("rightWidth"), 1501.23);
// test the number of hull points (should be equal)
TEST_EQUAL( mrmfeature.getFeature("1").getConvexHulls()[0].getHullPoints().size(), 7);
TEST_EQUAL( mrmfeature.getFeature("2").getConvexHulls()[0].getHullPoints().size(), 7);
