void FeatureGroupingAlgorithmQT::group_(const vector<MapType>& maps,
ConsensusMap& out)
{
// check that the number of maps is ok:
if (maps.size() < 2)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"At least two maps must be given!");
}
QTClusterFinder cluster_finder;
cluster_finder.setParameters(param_.copy("", true));
cluster_finder.run(maps, out);
StringList ms_run_locations;
// add protein IDs and unassigned peptide IDs to the result map here,
// to keep the same order as the input maps (useful for output later):
for (typename vector<MapType>::const_iterator map_it = maps.begin();
map_it != maps.end(); ++map_it)
{
// add protein identifications to result map:
out.getProteinIdentifications().insert(
out.getProteinIdentifications().end(),
map_it->getProteinIdentifications().begin(),
map_it->getProteinIdentifications().end());
// add unassigned peptide identifications to result map:
out.getUnassignedPeptideIdentifications().insert(
out.getUnassignedPeptideIdentifications().end(),
map_it->getUnassignedPeptideIdentifications().begin(),
map_it->getUnassignedPeptideIdentifications().end());
}
// canonical ordering for checking the results:
out.sortByQuality();
out.sortByMaps();
out.sortBySize();
return;
}
void FeatureGroupingAlgorithmUnlabeled::group(const std::vector<FeatureMap> & maps, ConsensusMap & out)
{
// check that the number of maps is ok
if (maps.size() < 2)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "At least two maps must be given!");
}
// define reference map (the one with most peaks)
Size reference_map_index = 0;
Size max_count = 0;
for (Size m = 0; m < maps.size(); ++m)
{
if (maps[m].size() > max_count)
{
max_count = maps[m].size();
reference_map_index = m;
}
}
std::vector<ConsensusMap> input(2);
// build a consensus map of the elements of the reference map (contains only singleton consensus elements)
MapConversion::convert(reference_map_index, maps[reference_map_index],
input[0]);
// loop over all other maps, extend the groups
StablePairFinder pair_finder;
pair_finder.setParameters(param_.copy("", true));
for (Size i = 0; i < maps.size(); ++i)
{
if (i != reference_map_index)
{
MapConversion::convert(i, maps[i], input[1]);
// compute the consensus of the reference map and map i
ConsensusMap result;
pair_finder.run(input, result);
input[0].swap(result);
}
}
// replace result with temporary map
out.swap(input[0]);
// copy back the input maps (they have been deleted while swapping)
out.getFileDescriptions() = input[0].getFileDescriptions();
// add protein IDs and unassigned peptide IDs to the result map here,
// to keep the same order as the input maps (useful for output later)
for (std::vector<FeatureMap>::const_iterator map_it = maps.begin();
map_it != maps.end(); ++map_it)
{
// add protein identifications to result map
out.getProteinIdentifications().insert(
out.getProteinIdentifications().end(),
map_it->getProteinIdentifications().begin(),
map_it->getProteinIdentifications().end());
// add unassigned peptide identifications to result map
out.getUnassignedPeptideIdentifications().insert(
out.getUnassignedPeptideIdentifications().end(),
map_it->getUnassignedPeptideIdentifications().begin(),
map_it->getUnassignedPeptideIdentifications().end());
}
// canonical ordering for checking the results, and the ids have no real meaning anyway
#if 1 // the way this was done in DelaunayPairFinder and StablePairFinder
out.sortByMZ();
#else
out.sortByQuality();
out.sortByMaps();
out.sortBySize();
#endif
return;
}
void LabeledPairFinder::run(const vector<ConsensusMap>& input_maps, ConsensusMap& result_map)
{
if (input_maps.size() != 1)
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "exactly one input map required");
if (result_map.getFileDescriptions().size() != 2)
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "two file descriptions required");
if (result_map.getFileDescriptions().begin()->second.filename != result_map.getFileDescriptions().rbegin()->second.filename)
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "the two file descriptions have to contain the same file name");
checkIds_(input_maps);
//look up the light and heavy index
Size light_index = numeric_limits<Size>::max();
Size heavy_index = numeric_limits<Size>::max();
for (ConsensusMap::FileDescriptions::const_iterator it = result_map.getFileDescriptions().begin();
it != result_map.getFileDescriptions().end();
++it)
{
if (it->second.label == "heavy")
{
heavy_index = it->first;
}
else if (it->second.label == "light")
{
light_index = it->first;
}
}
if (light_index == numeric_limits<Size>::max() || heavy_index == numeric_limits<Size>::max())
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "the input maps have to be labeled 'light' and 'heavy'");
}
result_map.clear(false);
// sort consensus features by RT (and MZ) to speed up searching afterwards
typedef ConstRefVector<ConsensusMap> RefMap;
RefMap model_ref(input_maps[0].begin(), input_maps[0].end());
model_ref.sortByPosition();
//calculate matches
ConsensusMap matches;
//settings
double rt_pair_dist = param_.getValue("rt_pair_dist");
double rt_dev_low = param_.getValue("rt_dev_low");
double rt_dev_high = param_.getValue("rt_dev_high");
double mz_dev = param_.getValue("mz_dev");
DoubleList mz_pair_dists = param_.getValue("mz_pair_dists");
bool mrm = param_.getValue("mrm").toBool();
//estimate RT parameters
if (param_.getValue("rt_estimate") == "true")
{
//find all possible RT distances of features with the same charge and a good m/z distance
vector<double> dists;
dists.reserve(model_ref.size());
for (RefMap::const_iterator it = model_ref.begin(); it != model_ref.end(); ++it)
{
for (RefMap::const_iterator it2 = model_ref.begin(); it2 != model_ref.end(); ++it2)
{
for (DoubleList::const_iterator dist_it = mz_pair_dists.begin(); dist_it != mz_pair_dists.end(); ++dist_it)
{
double mz_pair_dist = *dist_it;
if (it2->getCharge() == it->getCharge()
&& it2->getMZ() >= it->getMZ() + mz_pair_dist / it->getCharge() - mz_dev
&& it2->getMZ() <= it->getMZ() + mz_pair_dist / it->getCharge() + mz_dev)
{
dists.push_back(it2->getRT() - it->getRT());
}
}
}
}
if (dists.empty())
{
cout << "Warning: Could not find pairs for RT distance estimation. The manual settings are used!" << endl;
}
else
{
if (dists.size() < 50)
{
cout << "Warning: Found only " << dists.size() << " pairs. The estimated shift and std deviation are probably not reliable!" << endl;
}
//--------------------------- estimate initial parameters of fit ---------------------------
GaussFitter::GaussFitResult result(-1, -1, -1);
//first estimate of the optimal shift: median of the distances
sort(dists.begin(), dists.end());
Size median_index = dists.size() / 2;
result.x0 = dists[median_index];
//create histogram of distances
//consider only the maximum of pairs, centered around the optimal shift
Size max_pairs = model_ref.size() / 2;
Size start_index = (Size) max((SignedSize)0, (SignedSize)(median_index - max_pairs / 2));
Size end_index = (Size) min((SignedSize)(dists.size() - 1), (SignedSize)(median_index + max_pairs / 2));
double start_value = dists[start_index];
double end_value = dists[end_index];
double bin_step = fabs(end_value - start_value) / 99.999; //ensure that we have 100 bins
Math::Histogram<> hist(start_value, end_value, bin_step);
//std::cout << "HIST from " << start_value << " to " << end_value << " (bin size " << bin_step << ")" << endl;
for (Size i = start_index; i <= end_index; ++i)
{
hist.inc(dists[i]);
}
//cout << hist << endl;
dists.clear();
//determine median of bins (uniform background distribution)
vector<Size> bins(hist.begin(), hist.end());
sort(bins.begin(), bins.end());
Size bin_median = bins[bins.size() / 2];
bins.clear();
//estimate scale A: maximum of the histogram
Size max_value = hist.maxValue();
result.A = max_value - bin_median;
//overwrite estimate of x0 with the position of the highest bin
for (Size i = 0; i < hist.size(); ++i)
{
if (hist[i] == max_value)
{
result.x0 = hist.centerOfBin(i);
break;
}
}
//estimate sigma: first time the count is less or equal the median count in the histogram
double pos = result.x0;
while (pos > start_value && hist.binValue(pos) > bin_median)
{
pos -= bin_step;
}
double sigma_low = result.x0 - pos;
pos = result.x0;
while (pos<end_value&& hist.binValue(pos)> bin_median)
{
pos += bin_step;
}
double sigma_high = pos - result.x0;
result.sigma = (sigma_high + sigma_low) / 6.0;
//cout << "estimated optimal RT distance (before fit): " << result.x0 << endl;
//cout << "estimated allowed deviation (before fit): " << result.sigma*3.0 << endl;
//--------------------------- do gauss fit ---------------------------
vector<DPosition<2> > points(hist.size());
for (Size i = 0; i < hist.size(); ++i)
{
points[i][0] = hist.centerOfBin(i);
points[i][1] = max(0u, hist[i]);
}
GaussFitter fitter;
fitter.setInitialParameters(result);
result = fitter.fit(points);
cout << "estimated optimal RT distance: " << result.x0 << endl;
cout << "estimated allowed deviation: " << fabs(result.sigma) * 3.0 << endl;
rt_pair_dist = result.x0;
rt_dev_low = fabs(result.sigma) * 3.0;
rt_dev_high = fabs(result.sigma) * 3.0;
}
}
// check each feature
for (RefMap::const_iterator it = model_ref.begin(); it != model_ref.end(); ++it)
{
for (DoubleList::const_iterator dist_it = mz_pair_dists.begin(); dist_it != mz_pair_dists.end(); ++dist_it)
{
double mz_pair_dist = *dist_it;
RefMap::const_iterator it2 = lower_bound(model_ref.begin(), model_ref.end(), it->getRT() + rt_pair_dist - rt_dev_low, ConsensusFeature::RTLess());
while (it2 != model_ref.end() && it2->getRT() <= it->getRT() + rt_pair_dist + rt_dev_high)
{
// if in mrm mode, we need to compare precursor mass difference and fragment mass difference, charge remains the same
double prec_mz_diff(0);
if (mrm)
{
prec_mz_diff = fabs((double)it2->getMetaValue("MZ") - (double)it->getMetaValue("MZ"));
if (it->getCharge() != 0)
{
prec_mz_diff = fabs(prec_mz_diff - mz_pair_dist / it->getCharge());
}
else
{
prec_mz_diff = fabs(prec_mz_diff - mz_pair_dist);
}
}
bool mrm_correct_dist(false);
double frag_mz_diff = fabs(it->getMZ() - it2->getMZ());
//cerr << it->getRT() << " charge1=" << it->getCharge() << ", charge2=" << it2->getCharge() << ", prec_diff=" << prec_mz_diff << ", frag_diff=" << frag_mz_diff << endl;
if (mrm &&
it2->getCharge() == it->getCharge() &&
prec_mz_diff < mz_dev &&
(frag_mz_diff < mz_dev || fabs(frag_mz_diff - mz_pair_dist) < mz_dev))
{
mrm_correct_dist = true;
//cerr << "mrm_correct_dist" << endl;
}
if ((mrm && mrm_correct_dist) || (!mrm &&
it2->getCharge() == it->getCharge() &&
it2->getMZ() >= it->getMZ() + mz_pair_dist / it->getCharge() - mz_dev &&
it2->getMZ() <= it->getMZ() + mz_pair_dist / it->getCharge() + mz_dev
))
{
//cerr << "dist correct" << endl;
double score = sqrt(
PValue_(it2->getMZ() - it->getMZ(), mz_pair_dist / it->getCharge(), mz_dev, mz_dev) *
PValue_(it2->getRT() - it->getRT(), rt_pair_dist, rt_dev_low, rt_dev_high)
);
// Note: we used to copy the id from the light feature here, but that strategy does not generalize to more than two labels.
// We might want to report consensus features where the light one is missing but more than one heavier variant was found.
// Also, the old strategy is inconsistent with what was done in the unlabeled case. Thus now we assign a new unique id here.
matches.push_back(ConsensusFeature());
matches.back().setUniqueId();
matches.back().insert(light_index, *it);
matches.back().clearMetaInfo();
matches.back().insert(heavy_index, *it2);
matches.back().setQuality(score);
matches.back().setCharge(it->getCharge());
matches.back().computeMonoisotopicConsensus();
}
++it2;
}
}
}
//compute best pairs
// - sort matches by quality
// - take highest-quality matches first (greedy) and mark them as used
set<Size> used_features;
matches.sortByQuality(true);
for (ConsensusMap::const_iterator match = matches.begin(); match != matches.end(); ++match)
{
//check if features are not used yet
if (used_features.find(match->begin()->getUniqueId()) == used_features.end() &&
used_features.find(match->rbegin()->getUniqueId()) == used_features.end()
)
{
//if unused, add it to the final set of elements
result_map.push_back(*match);
used_features.insert(match->begin()->getUniqueId());
used_features.insert(match->rbegin()->getUniqueId());
}
}
//Add protein identifications to result map
for (Size i = 0; i < input_maps.size(); ++i)
{
result_map.getProteinIdentifications().insert(result_map.getProteinIdentifications().end(), input_maps[i].getProteinIdentifications().begin(), input_maps[i].getProteinIdentifications().end());
}
//Add unassigned peptide identifications to result map
for (Size i = 0; i < input_maps.size(); ++i)
{
result_map.getUnassignedPeptideIdentifications().insert(result_map.getUnassignedPeptideIdentifications().end(), input_maps[i].getUnassignedPeptideIdentifications().begin(), input_maps[i].getUnassignedPeptideIdentifications().end());
}
// Very useful for checking the results, and the ids have no real meaning anyway
result_map.sortByMZ();
}