| OpenMS 2.5.0

QTCluster.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
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10 // * Redistributions in binary form must reproduce the above copyright
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Steffen Sass, Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/CHEMISTRY/AASequence.h>
40 #include <OpenMS/OpenMSConfig.h>
41 #include <OpenMS/config.h>
42
43 #include <boost/unordered_map.hpp>
44
45 #include <map> // for multimap<>
46 #include <vector> // for vector<>
47 #include <set> // for set<>
48 #include <utility> // for pair<>
49
50
51 namespace OpenMS
52 {
53 class GridFeature;
54
55 // Boost switch since with 1.47 several classes got moved into a new
56 // boost::unordered namespace (specifically unordered_map).
57 namespace OpenMSBoost
58 {
59 #if OPENMS_BOOST_VERSION_MINOR > 47
60 using namespace boost::unordered;
61 #else
62 using namespace boost;
63 #endif
64 }
65
66
111 class OPENMS_DLLAPI QTCluster
112 {
113 private:
114
115 // need to store more than one
116 typedef std::multimap<double, GridFeature*> NeighborListType;
117 typedef OpenMSBoost::unordered_map<Size, NeighborListType> NeighborMapMulti;
118
119 typedef std::pair<double, GridFeature*> NeighborPairType;
120 typedef OpenMSBoost::unordered_map<Size, NeighborPairType> NeighborMap;
121
123 GridFeature* center_point_;
124
129 NeighborMap neighbors_;
130
138 NeighborMapMulti* tmp_neighbors_;
139
141 double max_distance_;
142
144 Size num_maps_;
145
147 double quality_;
148
150 bool changed_;
151
153 bool use_IDs_;
154
156 bool valid_;
157
167 bool collect_annotations_;
168
170 bool finalized_;
171
173 Int x_coord_;
174
176 Int y_coord_;
177
184 std::set<AASequence> annotations_;
185
187 QTCluster();
188
190 void computeQuality_();
191
211 double optimizeAnnotations_();
212
213 public:
214
222 QTCluster(GridFeature* center_point, Size num_maps,
223 double max_distance, bool use_IDs,
224 Int x_coord, Int y_coord);
225
227 virtual ~QTCluster();
228
230 GridFeature* getCenterPoint();
231
233 double getCenterRT() const;
234
236 double getCenterMZ() const;
237
239 Int getXCoord() const;
240
242 Int getYCoord() const;
243
245 Size size() const;
246
248 bool operator<(QTCluster& cluster);
249
256 void add(GridFeature* element, double distance);
257
259 void getElements(OpenMSBoost::unordered_map<Size, GridFeature*>& elements);
260
268 bool update(const OpenMSBoost::unordered_map<Size, GridFeature*>& removed);
269
271 double getQuality();
272
274 const std::set<AASequence>& getAnnotations();
275
283 void setInvalid();
284
286 inline bool isInvalid() const
287 {
288 return !valid_;
289 }
290
292 void initializeCluster();
293
295 void finalizeCluster();
296
298 OpenMSBoost::unordered_map<Size, std::vector<GridFeature*> > getAllNeighbors();
299 };
300 } // namespace OpenMS
301
OpenMS::QTCluster::max_distance_
double max_distance_
Maximum distance of a point that can still belong to the cluster.
Definition: QTCluster.h:141
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::QTCluster::quality_
double quality_
Quality of the cluster.
Definition: QTCluster.h:147
AASequence.h
OpenMS::QTCluster::y_coord_
Int y_coord_
y coordinate in the grid cell
Definition: QTCluster.h:176
OpenMS::QTCluster::changed_
bool changed_
Has the cluster changed (if yes, quality needs to be recomputed)?
Definition: QTCluster.h:150
Types.h
OpenMS::GridFeature
Representation of a feature in a hash grid.
Definition: GridFeature.h:52
OpenMS::QTCluster
A representation of a QT cluster used for feature grouping.
Definition: QTCluster.h:111
OpenMS::QTCluster::isInvalid
bool isInvalid() const
Whether current cluster is invalid.
Definition: QTCluster.h:286
boost
OpenMS::QTCluster::NeighborMap
OpenMSBoost::unordered_map< Size, NeighborPairType > NeighborMap
Definition: QTCluster.h:120
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::QTCluster::use_IDs_
bool use_IDs_
Keep track of peptide IDs and use them for matching?
Definition: QTCluster.h:153
OpenMS::QTCluster::annotations_
std::set< AASequence > annotations_
Set of annotations of the cluster.
Definition: QTCluster.h:184
OpenMS::QTCluster::NeighborMapMulti
OpenMSBoost::unordered_map< Size, NeighborListType > NeighborMapMulti
Definition: QTCluster.h:117
OpenMS::QTCluster::num_maps_
Size num_maps_
Number of input maps.
Definition: QTCluster.h:144
OpenMS::QTCluster::valid_
bool valid_
Whether current cluster is valid.
Definition: QTCluster.h:156
OpenMS::QTCluster::x_coord_
Int x_coord_
x coordinate in the grid cell
Definition: QTCluster.h:173
OpenMS::QTCluster::center_point_
GridFeature * center_point_
Pointer to the cluster center.
Definition: QTCluster.h:123
int
OpenMS::QTCluster::NeighborListType
std::multimap< double, GridFeature * > NeighborListType
Definition: QTCluster.h:116
OpenMS::QTCluster::neighbors_
NeighborMap neighbors_
Map that keeps track of the best current feature for each map.
Definition: QTCluster.h:129
OpenMS::QTCluster::collect_annotations_
bool collect_annotations_
Whether initial collection of all neighbors is needed.
Definition: QTCluster.h:167
OpenMS::QTCluster::NeighborPairType
std::pair< double, GridFeature * > NeighborPairType
Definition: QTCluster.h:119
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::QTCluster::tmp_neighbors_
NeighborMapMulti * tmp_neighbors_
Temporary map tracking *all* neighbors.
Definition: QTCluster.h:138
OpenMS::QTCluster::finalized_
bool finalized_
Whether current cluster is accepting new elements or not (if true, no more new elements allowed) ...
Definition: QTCluster.h:170