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OpenMS
2.6.0
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40 #include <OpenMS/OpenMSConfig.h>
41 #include <OpenMS/config.h>
43 #include <boost/unordered_map.hpp>
58 #if OPENMS_BOOST_VERSION_MINOR > 47
59 using namespace boost::unordered;
61 using namespace boost;
154 Size num_maps,
double max_distance,
242 double getCenterRT()
const;
245 double getCenterMZ()
const;
248 Int getXCoord()
const;
251 Int getYCoord()
const;
265 void add(
const GridFeature*
const element,
double distance);
277 bool update(
const Elements& removed);
283 double getCurrentQuality()
const;
286 const std::set<AASequence>& getAnnotations();
304 void initializeCluster();
307 void finalizeCluster();
310 Elements getAllNeighbors()
const;
314 void computeQuality_();
335 double optimizeAnnotations_();
338 void makeSeqTable_(std::map<std::set<AASequence>, std::vector<double>>& seq_table)
const;
341 void recomputeNeighbors_();
void removeAttachment(String r, std::vector< String > &ids, String at="")
Removes attachments referencing a id given in ids, from run/set r. All attachments if no attachment n...
Base class for TOPP applications.
Definition: TOPPBase.h:144
Int y_coord_
y coordinate in the grid cell
Definition: QTCluster.h:190
std::set< AASequence > annotations_
Set of annotations of the cluster.
Definition: QTCluster.h:198
Size id_
unique id of this cluster
Definition: QTCluster.h:163
Definition: QTCluster.h:118
A more convenient string class.
Definition: String.h:59
bool isInvalid() const
Whether current cluster is invalid.
Definition: QTCluster.h:298
OpenMSBoost::unordered_map< Size, Neighbor > NeighborMap
Definition: QTCluster.h:124
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
void removeAllAttachments(String at)
Removes attachment with cv accession at from all runs/sets.
bool finalized_
Whether current cluster is accepting new elements or not (if true, no more new elements allowed)
Definition: QTCluster.h:370
std::vector< Element > Elements
Definition: QTCluster.h:132
Definition: QTCluster.h:126
Representation of a feature in a hash grid.
Definition: GridFeature.h:52
bool operator<(const QTCluster &q1, const QTCluster &q2)
void load(const String &filename)
Load a QCFile.
void store(const String &filename) const
Store the QCFile.
Size map_index
Definition: QTCluster.h:128
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
A representation of a QT cluster used for feature grouping.
Definition: QTCluster.h:110
bool changed_
Has the cluster changed (if yes, quality needs to be recomputed)?
Definition: QTCluster.h:353
std::multimap< double, const GridFeature * > NeighborList
Definition: QTCluster.h:115
Size num_maps_
Number of input maps.
Definition: QTCluster.h:184
bool collect_annotations_
Whether initial collection of all neighbors is needed.
Definition: QTCluster.h:367
bool valid_
Whether current cluster is valid.
Definition: QTCluster.h:350
bool use_IDs_
Keep track of peptide IDs and use them for matching?
Definition: QTCluster.h:356
BulkData * data_
Pointer to data members.
Definition: QTCluster.h:347
double max_distance_
Maximum distance of a point that can still belong to the cluster.
Definition: QTCluster.h:181
OpenMSBoost::unordered_map< Size, NeighborList > NeighborMapMulti
Definition: QTCluster.h:116
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
const GridFeature *const center_point_
Pointer to the cluster center.
Definition: QTCluster.h:160
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
Class to store the bulk internal data (neighbors, annotations, etc.)
Definition: QTCluster.h:140
NeighborMapMulti tmp_neighbors_
Temporary map tracking *all* neighbors.
Definition: QTCluster.h:178
File adapter for QcML files used to load and store QcML files.
Definition: QcMLFile.h:57
NeighborMap neighbors_
Map that keeps track of the best current feature for each map.
Definition: QTCluster.h:169
const GridFeature * feature
Definition: QTCluster.h:121
double distance
Definition: QTCluster.h:120
Int x_coord_
x coordinate in the grid cell
Definition: QTCluster.h:187
double quality_
Quality of the cluster.
Definition: QTCluster.h:344