void FeatureGroupingAlgorithm::transferSubelements(const vector<ConsensusMap>& maps, ConsensusMap& out) const
{
// accumulate file descriptions from the input maps:
// cout << "Updating file descriptions..." << endl;
out.getFileDescriptions().clear();
// mapping: (map index, original id) -> new id
map<pair<Size, UInt64>, Size> mapid_table;
for (Size i = 0; i < maps.size(); ++i)
{
const ConsensusMap& consensus = maps[i];
for (ConsensusMap::FileDescriptions::const_iterator desc_it = consensus.getFileDescriptions().begin(); desc_it != consensus.getFileDescriptions().end(); ++desc_it)
{
Size counter = mapid_table.size();
mapid_table[make_pair(i, desc_it->first)] = counter;
out.getFileDescriptions()[counter] = desc_it->second;
}
}
// look-up table: input map -> unique ID -> consensus feature
// cout << "Creating look-up table..." << endl;
vector<map<UInt64, ConsensusMap::ConstIterator> > feat_lookup(maps.size());
for (Size i = 0; i < maps.size(); ++i)
{
const ConsensusMap& consensus = maps[i];
for (ConsensusMap::ConstIterator feat_it = consensus.begin();
feat_it != consensus.end(); ++feat_it)
{
// do NOT use "id_lookup[i][feat_it->getUniqueId()] = feat_it;" here as
// you will get "attempt to copy-construct an iterator from a singular
// iterator" in STL debug mode:
feat_lookup[i].insert(make_pair(feat_it->getUniqueId(), feat_it));
}
}
// adjust the consensus features:
// cout << "Adjusting consensus features..." << endl;
for (ConsensusMap::iterator cons_it = out.begin(); cons_it != out.end(); ++cons_it)
{
ConsensusFeature adjusted = ConsensusFeature(
static_cast<BaseFeature>(*cons_it)); // remove sub-features
for (ConsensusFeature::HandleSetType::const_iterator sub_it = cons_it->getFeatures().begin(); sub_it != cons_it->getFeatures().end(); ++sub_it)
{
UInt64 id = sub_it->getUniqueId();
Size map_index = sub_it->getMapIndex();
ConsensusMap::ConstIterator origin = feat_lookup[map_index][id];
for (ConsensusFeature::HandleSetType::const_iterator handle_it = origin->getFeatures().begin(); handle_it != origin->getFeatures().end(); ++handle_it)
{
FeatureHandle handle = *handle_it;
Size new_id = mapid_table[make_pair(map_index, handle.getMapIndex())];
handle.setMapIndex(new_id);
adjusted.insert(handle);
}
}
*cons_it = adjusted;
}
}
void StablePairFinder::run(const std::vector<ConsensusMap>& input_maps,
ConsensusMap& result_map)
{
// empty output destination:
result_map.clear(false);
// sanity checks:
if (input_maps.size() != 2)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"exactly two input maps required");
}
checkIds_(input_maps);
// set up the distance functor:
double max_intensity = max(input_maps[0].getMaxInt(),
input_maps[1].getMaxInt());
Param distance_params = param_.copy("");
distance_params.remove("use_identifications");
distance_params.remove("second_nearest_gap");
FeatureDistance feature_distance(max_intensity, false);
feature_distance.setParameters(distance_params);
// keep track of pairing:
std::vector<bool> is_singleton[2];
is_singleton[0].resize(input_maps[0].size(), true);
is_singleton[1].resize(input_maps[1].size(), true);
typedef pair<double, double> DoublePair;
DoublePair init = make_pair(FeatureDistance::infinity,
FeatureDistance::infinity);
// for every element in map 0:
// - index of nearest neighbor in map 1:
vector<UInt> nn_index_0(input_maps[0].size(), UInt(-1));
// - distances to nearest and second-nearest neighbors in map 1:
vector<DoublePair> nn_distance_0(input_maps[0].size(), init);
// for every element in map 1:
// - index of nearest neighbor in map 0:
vector<UInt> nn_index_1(input_maps[1].size(), UInt(-1));
// - distances to nearest and second-nearest neighbors in map 0:
vector<DoublePair> nn_distance_1(input_maps[1].size(), init);
// iterate over all feature pairs, find nearest neighbors:
// TODO: iterate over SENSIBLE RT (and m/z) window -- sort the maps beforehand
// to save a lot of processing time...
// Once done, remove the warning in the description of the 'use_identifications' parameter
for (UInt fi0 = 0; fi0 < input_maps[0].size(); ++fi0)
{
const ConsensusFeature& feat0 = input_maps[0][fi0];
for (UInt fi1 = 0; fi1 < input_maps[1].size(); ++fi1)
{
const ConsensusFeature& feat1 = input_maps[1][fi1];
if (use_IDs_ && !compatibleIDs_(feat0, feat1)) // check peptide IDs
{
continue; // mismatch
}
pair<bool, double> result = feature_distance(feat0, feat1);
double distance = result.second;
// we only care if distance constraints are satisfied for "best
// matches", not for second-best; this means that second-best distances
// can become smaller than best distances
// (e.g. the RT is larger than allowed (->invalid pair), but m/z is perfect and has the most weight --> better score!)
bool valid = result.first;
// update entries for map 0:
if (distance < nn_distance_0[fi0].second)
{
if (valid && (distance < nn_distance_0[fi0].first))
{
nn_distance_0[fi0].second = nn_distance_0[fi0].first;
nn_distance_0[fi0].first = distance;
nn_index_0[fi0] = fi1;
}
else
{
nn_distance_0[fi0].second = distance;
}
}
// update entries for map 1:
if (distance < nn_distance_1[fi1].second)
{
if (valid && (distance < nn_distance_1[fi1].first))
{
nn_distance_1[fi1].second = nn_distance_1[fi1].first;
nn_distance_1[fi1].first = distance;
nn_index_1[fi1] = fi0;
}
else
{
nn_distance_1[fi1].second = distance;
}
}
}
}
// if features from the two maps are nearest neighbors of each other, they
// can become a pair:
for (UInt fi0 = 0; fi0 < input_maps[0].size(); ++fi0)
{
UInt fi1 = nn_index_0[fi0]; // nearest neighbor of "fi0" in map 1
// cout << "index: " << fi0 << ", RT: " << input_maps[0][fi0].getRT()
// << ", MZ: " << input_maps[0][fi0].getMZ() << endl
// << "neighbor: " << fi1 << ", RT: " << input_maps[1][fi1].getRT()
// << ", MZ: " << input_maps[1][fi1].getMZ() << endl
// << "d(i,j): " << nn_distance_0[fi0].first << endl
// << "d2(i): " << nn_distance_0[fi0].second << endl
// << "d2(j): " << nn_distance_1[fi1].second << endl;
// criteria set by the parameters must be fulfilled:
if ((nn_distance_0[fi0].first < FeatureDistance::infinity) &&
(nn_distance_0[fi0].first * second_nearest_gap_ <= nn_distance_0[fi0].second))
{
// "fi0" satisfies constraints...
if ((nn_index_1[fi1] == fi0) &&
(nn_distance_1[fi1].first * second_nearest_gap_ <= nn_distance_1[fi1].second))
{
// ...nearest neighbor of "fi0" also satisfies constraints (yay!)
// cout << "match!" << endl;
result_map.push_back(ConsensusFeature());
ConsensusFeature& f = result_map.back();
f.insert(input_maps[0][fi0]);
f.getPeptideIdentifications().insert(f.getPeptideIdentifications().end(),
input_maps[0][fi0].getPeptideIdentifications().begin(),
input_maps[0][fi0].getPeptideIdentifications().end());
f.insert(input_maps[1][fi1]);
f.getPeptideIdentifications().insert(f.getPeptideIdentifications().end(),
input_maps[1][fi1].getPeptideIdentifications().begin(),
input_maps[1][fi1].getPeptideIdentifications().end());
f.computeConsensus();
double quality = 1.0 - nn_distance_0[fi0].first;
double quality0 = 1.0 - nn_distance_0[fi0].first * second_nearest_gap_ / nn_distance_0[fi0].second;
double quality1 = 1.0 - nn_distance_1[fi1].first * second_nearest_gap_ / nn_distance_1[fi1].second;
quality = quality * quality0 * quality1; // TODO other formula?
// incorporate existing quality values:
Size size0 = max(input_maps[0][fi0].size(), size_t(1));
Size size1 = max(input_maps[1][fi1].size(), size_t(1));
// quality contribution from first map:
quality0 = input_maps[0][fi0].getQuality() * (size0 - 1);
// quality contribution from second map:
quality1 = input_maps[1][fi1].getQuality() * (size1 - 1);
f.setQuality((quality + quality0 + quality1) / (size0 + size1 - 1));
is_singleton[0][fi0] = false;
is_singleton[1][fi1] = false;
}
}
}
// write out unmatched consensus features
for (UInt input = 0; input <= 1; ++input)
{
for (UInt index = 0; index < input_maps[input].size(); ++index)
{
if (is_singleton[input][index])
{
result_map.push_back(input_maps[input][index]);
if (result_map.back().size() < 2) // singleton consensus feature
{
result_map.back().setQuality(0.0);
}
}
}
}
// canonical ordering for checking the results, and the ids have no real meaning anyway
result_map.sortByMZ();
// protein IDs and unassigned peptide IDs are added to the result by the
// FeatureGroupingAlgorithm!
}
