FeatureHandle::FeatureHandle(UInt64 map_index, const BaseFeature& feature) :
Peak2D(feature),
UniqueIdInterface(feature),
map_index_(map_index),
charge_(feature.getCharge()),
width_(feature.getWidth())
{
}
void MapAlignmentTransformer::applyToBaseFeature_(BaseFeature & feature,
const TransformationDescription & trafo)
{
// transform feature position:
DoubleReal rt = feature.getRT();
feature.setRT(trafo.apply(rt));
// adapt RT values of annotated peptides:
if (!feature.getPeptideIdentifications().empty())
{
transformSinglePeptideIdentification(feature.getPeptideIdentifications(),
trafo);
}
}
void MapAlignmentTransformer::applyToBaseFeature_(
BaseFeature& feature, const TransformationDescription& trafo,
bool store_original_rt)
{
// transform feature position:
double rt = feature.getRT();
if (store_original_rt) storeOriginalRT_(feature, rt);
feature.setRT(trafo.apply(rt));
// adapt RT values of annotated peptides:
if (!feature.getPeptideIdentifications().empty())
{
transformRetentionTimes(feature.getPeptideIdentifications(), trafo,
store_original_rt);
}
}
GridFeature::GridFeature(const BaseFeature& feature, Size map_index,
Size feature_index) :
feature_(feature),
map_index_(map_index),
feature_index_(feature_index),
annotations_()
{
const vector<PeptideIdentification>& peptides =
feature.getPeptideIdentifications();
for (vector<PeptideIdentification>::const_iterator pep_it =
peptides.begin(); pep_it != peptides.end(); ++pep_it)
{
if (pep_it->getHits().empty())
continue; // shouldn't be the case
annotations_.insert(pep_it->getHits()[0].getSequence());
}
}
pair<bool, DoubleReal> FeatureDistance::operator()(const BaseFeature & left,
const BaseFeature & right)
{
if (!ignore_charge_)
{
Int charge_left = left.getCharge(), charge_right = right.getCharge();
if (charge_left != charge_right)
{
if ((charge_left != 0) && (charge_right != 0))
{
return make_pair(false, infinity);
}
}
}
bool valid = true;
// check m/z difference constraint:
DoubleReal left_mz = left.getMZ(), right_mz = right.getMZ();
DoubleReal dist_mz = fabs(left_mz - right_mz);
DoubleReal max_diff_mz = params_mz_.max_difference;
if (params_mz_.max_diff_ppm) // compute absolute difference (in Da/Th)
{
max_diff_mz *= left_mz * 1e-6;
// overwrite this parameter - it will be recomputed each time anyway:
params_mz_.norm_factor = 1 / max_diff_mz;
}
if (dist_mz > max_diff_mz)
{
if (force_constraints_)
{
return make_pair(false, infinity);
}
valid = false;
}
// check RT difference constraint:
DoubleReal dist_rt = fabs(left.getRT() - right.getRT());
if (dist_rt > params_rt_.max_difference)
{
if (force_constraints_)
{
return make_pair(false, infinity);
}
valid = false;
}
dist_rt = distance_(dist_rt, params_rt_);
dist_mz = distance_(dist_mz, params_mz_);
DoubleReal dist_intensity = 0.0;
if (params_intensity_.relevant) // not by default, so worth checking
{
dist_intensity = fabs(left.getIntensity() - right.getIntensity());
dist_intensity = distance_(dist_intensity, params_intensity_);
}
DoubleReal dist = dist_rt + dist_mz + dist_intensity;
dist *= total_weight_reciprocal_;
return make_pair(valid, dist);
}