void MapAlignmentTransformer::applyToFeature_(Feature & feature,
const TransformationDescription & trafo)
{
applyToBaseFeature_(feature, trafo);
// loop over all convex hulls
vector<ConvexHull2D> & convex_hulls = feature.getConvexHulls();
for (vector<ConvexHull2D>::iterator chiter = convex_hulls.begin();
chiter != convex_hulls.end(); ++chiter)
{
// transform all hull point positions within convex hull
ConvexHull2D::PointArrayType points = chiter->getHullPoints();
chiter->clear();
for (ConvexHull2D::PointArrayType::iterator points_iter = points.begin();
points_iter != points.end();
++points_iter
)
{
DoubleReal rt = (*points_iter)[Feature::RT];
(*points_iter)[Feature::RT] = trafo.apply(rt);
}
chiter->setHullPoints(points);
}
// recurse into subordinates
for (vector<Feature>::iterator subiter = feature.getSubordinates().begin();
subiter != feature.getSubordinates().end();
++subiter)
{
applyToFeature_(*subiter, trafo);
}
}
void MapAlignmentTransformer::transformSingleFeatureMap(FeatureMap<> & fmap,
const TransformationDescription & trafo)
{
for (vector<Feature>::iterator fmit = fmap.begin(); fmit != fmap.end(); ++fmit)
{
applyToFeature_(*fmit, trafo);
}
// adapt RT values of unassigned peptides:
if (!fmap.getUnassignedPeptideIdentifications().empty())
{
transformSinglePeptideIdentification(
fmap.getUnassignedPeptideIdentifications(), trafo);
}
}
void MapAlignmentTransformer::transformRetentionTimes(
FeatureMap& fmap, const TransformationDescription& trafo,
bool store_original_rt)
{
for (vector<Feature>::iterator fmit = fmap.begin(); fmit != fmap.end();
++fmit)
{
applyToFeature_(*fmit, trafo, store_original_rt);
}
// adapt RT values of unassigned peptides:
if (!fmap.getUnassignedPeptideIdentifications().empty())
{
transformRetentionTimes(fmap.getUnassignedPeptideIdentifications(), trafo,
store_original_rt);
}
}
