35 #ifndef OPENMS_ANALYSIS_MAPMATCHING_QTCLUSTERFINDER_H 36 #define OPENMS_ANALYSIS_MAPMATCHING_QTCLUSTERFINDER_H 45 #include <boost/unordered_map.hpp> 110 typedef OpenMSBoost::unordered_map<
111 std::pair<OpenMS::GridFeature*, OpenMS::GridFeature*>,
115 typedef OpenMSBoost::unordered_map<
148 void setParameters_(
double max_intensity,
double max_mz);
151 void makeConsensusFeature_(std::list<QTCluster>& clustering,
153 ElementMapping& element_mapping, Grid&);
156 void computeClustering_(Grid& grid, std::list<QTCluster>& clustering);
159 template <
typename MapType>
160 void run_(
const std::vector<MapType>& input_maps,
ConsensusMap& result_map);
163 template <
typename MapType>
164 void run_internal_(
const std::vector<MapType>& input_maps,
168 void addClusterElements_(
int x,
int y,
const Grid& grid,
QTCluster& cluster,
200 void run(
const std::vector<ConsensusMap>& input_maps,
210 void run(
const std::vector<FeatureMap>& input_maps,
Container for (2-dimensional coordinate, value) pairs.
Definition: HashGrid.h:62
FeatureDistance feature_distance_
Feature distance functor.
Definition: QTClusterFinder.h:136
A functor class for the calculation of distances between features or consensus features.
Definition: FeatureDistance.h:90
A more convenient string class.
Definition: String.h:57
static BaseGroupFinder * create()
Returns an instance of this class.
Definition: QTClusterFinder.h:214
std::set< OpenMS::GridFeature * > already_used_
Set of features already used.
Definition: QTClusterFinder.h:139
A representation of a QT cluster used for feature grouping.
Definition: QTCluster.h:112
Retention time dimension id (0 if used as a const int)
Definition: Peak2D.h:76
bool use_IDs_
Consider peptide identifications for grouping?
Definition: QTClusterFinder.h:124
A container for consensus elements.
Definition: ConsensusMap.h:72
double max_diff_mz_
Maximum m/z difference.
Definition: QTClusterFinder.h:130
static const String getProductName()
Returns the name of the product.
Definition: QTClusterFinder.h:188
Mass-to-charge dimension id (1 if used as a const int)
Definition: Peak2D.h:77
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Size num_maps_
Number of input maps.
Definition: QTClusterFinder.h:121
HashGrid< OpenMS::GridFeature * > Grid
Definition: QTClusterFinder.h:118
double max_diff_rt_
Maximum RT difference.
Definition: QTClusterFinder.h:127
The base class of all element group finding algorithms.
Definition: BaseGroupFinder.h:62
OpenMSBoost::unordered_map< OpenMS::GridFeature *, std::vector< QTCluster * > > ElementMapping
Map to store which grid features are next to which clusters.
Definition: QTClusterFinder.h:116
Representation of a feature in a hash grid.
Definition: GridFeature.h:53
int nr_partitions_
Maximum m/z difference.
Definition: QTClusterFinder.h:133
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
OpenMSBoost::unordered_map< std::pair< OpenMS::GridFeature *, OpenMS::GridFeature * >, double > PairDistances
Distances between pairs of grid features.
Definition: QTClusterFinder.h:112
A variant of QT clustering for the detection of feature groups.
Definition: QTClusterFinder.h:104
A 2-dimensional consensus feature.
Definition: ConsensusFeature.h:65