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());
}
}