OpenMS
QTCluster.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Steffen Sass, Hendrik Weisser $
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34 
35 
36 #pragma once
37 
38 #include <OpenMS/CONCEPT/Types.h>
40 #include <OpenMS/OpenMSConfig.h>
41 #include <OpenMS/config.h>
42 
43 #include <unordered_map>
44 
45 #include <map> // for multimap<>
46 #include <vector> // for vector<>
47 #include <set> // for set<>
48 #include <utility> // for pair<>
49 
50 namespace OpenMS
51 {
52  class GridFeature;
53 
107  class OPENMS_DLLAPI QTCluster
108  {
109 public:
110 
111  // need to store more than one
112  typedef std::multimap<double, const GridFeature*> NeighborList;
113  typedef std::unordered_map<Size, NeighborList> NeighborMapMulti;
114 
115  struct Neighbor
116  {
117  double distance;
119  };
120 
121  typedef std::unordered_map<Size, Neighbor> NeighborMap;
122 
123  struct Element
124  {
127  };
128 
129  typedef std::vector<Element> Elements;
130 
137  class OPENMS_DLLAPI BulkData
138  {
139  friend class QTCluster;
140 
141  public:
142 
150  BulkData(const OpenMS::GridFeature* const center_point,
151  Size num_maps, double max_distance,
152  Int x_coord, Int y_coord, Size id);
153 
154  private:
155 
158 
161 
167 
176 
179 
182 
185 
188 
195  std::set<AASequence> annotations_;
196  };
197 
204  QTCluster(BulkData* const data, bool use_IDs);
205 
211  QTCluster() = delete;
212 
219  QTCluster(const QTCluster& rhs) = default;
220 
222  QTCluster& operator=(const QTCluster& rhs) = default;
223 
225  QTCluster(QTCluster&& rhs) = default;
226 
228  QTCluster& operator=(QTCluster&& rhs) = default;
229 
230  ~QTCluster() = default;
231 
233  const GridFeature* getCenterPoint() const;
234 
236  Size getId() const;
237 
239  double getCenterRT() const;
240 
242  double getCenterMZ() const;
243 
245  Int getXCoord() const;
246 
248  Int getYCoord() const;
249 
251  Size size() const;
252 
254  bool operator<(const QTCluster& cluster) const;
255 
262  void add(const GridFeature* const element, double distance);
263 
266 
274  bool update(const Elements& removed);
275 
277  double getQuality();
278 
280  double getCurrentQuality() const;
281 
283  const std::set<AASequence>& getAnnotations();
284 
292  void setInvalid();
293 
295  inline bool isInvalid() const
296  {
297  return !valid_;
298  }
299 
302 
305 
308 
309  private:
312 
333 
335  void makeSeqTable_(std::map<AASequence, std::map<Size,double>>& seq_table) const;
336 
339 
341  double quality_;
342 
345 
347  bool valid_;
348 
350  bool changed_;
351 
353  bool use_IDs_;
354 
365 
368  };
369 
370 } // namespace OpenMS
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Representation of a feature in a hash grid.
Definition: GridFeature.h:53
Class to store the bulk internal data (neighbors, annotations, etc.)
Definition: QTCluster.h:138
NeighborMapMulti tmp_neighbors_
Temporary map tracking *all* neighbors.
Definition: QTCluster.h:175
BulkData(const OpenMS::GridFeature *const center_point, Size num_maps, double max_distance, Int x_coord, Int y_coord, Size id)
Detailed constructor of the cluster body.
Int x_coord_
x coordinate in the grid cell
Definition: QTCluster.h:184
const GridFeature *const center_point_
Pointer to the cluster center.
Definition: QTCluster.h:157
std::set< AASequence > annotations_
Set of annotations of the cluster.
Definition: QTCluster.h:195
NeighborMap neighbors_
Map that keeps track of the best current feature for each map.
Definition: QTCluster.h:166
Size num_maps_
Number of input maps.
Definition: QTCluster.h:181
Int y_coord_
y coordinate in the grid cell
Definition: QTCluster.h:187
double max_distance_
Maximum distance of a point that can still belong to the cluster.
Definition: QTCluster.h:178
Size id_
unique id of this cluster
Definition: QTCluster.h:160
A representation of a QT cluster used for feature grouping.
Definition: QTCluster.h:108
std::vector< Element > Elements
Definition: QTCluster.h:129
const std::set< AASequence > & getAnnotations()
Return the set of peptide sequences annotated to the cluster center.
void setInvalid()
Sets current cluster as invalid (also frees some memory)
Int getXCoord() const
Returns the x coordinate in the grid.
void initializeCluster()
Has to be called before adding elements (calling QTCluster::add)
double getCurrentQuality() const
Returns the cluster quality without recomputing.
QTCluster(const QTCluster &rhs)=default
Cheap copy ctor because most of the data lies outside of this class (BulkData*) Be very careful with ...
bool isInvalid() const
Whether current cluster is invalid.
Definition: QTCluster.h:295
bool valid_
Whether current cluster is valid.
Definition: QTCluster.h:347
void add(const GridFeature *const element, double distance)
Adds a new element/neighbor to the cluster.
double quality_
Quality of the cluster.
Definition: QTCluster.h:341
bool collect_annotations_
Whether initial collection of all neighbors is needed.
Definition: QTCluster.h:364
QTCluster & operator=(const QTCluster &rhs)=default
Cheap copy assignment, see copy ctor for details.
bool operator<(const QTCluster &cluster) const
Compare by quality.
void recomputeNeighbors_()
report elements that are compatible with the optimal annotation
const GridFeature * getCenterPoint() const
Returns the cluster center.
void makeSeqTable_(std::map< AASequence, std::map< Size, double >> &seq_table) const
compute seq table, mapping: peptides -> best distance per input map
std::multimap< double, const GridFeature * > NeighborList
Definition: QTCluster.h:112
Size map_index
Definition: QTCluster.h:125
Size getId() const
returns the clusters id
void finalizeCluster()
Has to be called after adding elements (after calling QTCluster::add one or multiple times)
double distance
Definition: QTCluster.h:117
BulkData * data_
Pointer to data members.
Definition: QTCluster.h:344
double optimizeAnnotations_()
Finds the optimal annotation (peptide sequences) for the cluster.
~QTCluster()=default
Elements getAllNeighbors() const
Get all current neighbors.
bool changed_
Has the cluster changed (if yes, quality needs to be recomputed)?
Definition: QTCluster.h:350
bool use_IDs_
Keep track of peptide IDs and use them for matching?
Definition: QTCluster.h:353
std::unordered_map< Size, NeighborList > NeighborMapMulti
Definition: QTCluster.h:113
bool update(const Elements &removed)
Updates the cluster after the indicated data points are removed.
Size size() const
Returns the size of the cluster (number of elements, incl. center)
QTCluster(BulkData *const data, bool use_IDs)
Detailed constructor of the cluster head.
double getQuality()
Returns the cluster quality and recomputes if necessary.
double getCenterMZ() const
Returns the m/z value of the cluster center.
QTCluster(QTCluster &&rhs)=default
cheap move ctor because most of the data lies outside of this class (BulkData*)
QTCluster & operator=(QTCluster &&rhs)=default
cheap move assignment because most of the data lies outside of this class (BulkData*)
Int getYCoord() const
Returns the y coordinate in the grid.
double getCenterRT() const
Returns the RT value of the cluster.
bool finalized_
Whether current cluster is accepting new elements or not (if true, no more new elements allowed)
Definition: QTCluster.h:367
const GridFeature * feature
Definition: QTCluster.h:118
void computeQuality_()
Computes the quality of the cluster.
QTCluster()=delete
Default constructor not accessible Objects of this class should only exist with a valid BulkData* giv...
Elements getElements() const
Gets the clustered elements meaning neighbors + cluster center.
std::unordered_map< Size, Neighbor > NeighborMap
Definition: QTCluster.h:121
Definition: QTCluster.h:124
Definition: QTCluster.h:116
int Int
Signed integer type.
Definition: Types.h:102
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48