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NSPDK_port.hh
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1 /*
2  * NSPDK_port.hh
3  *
4  * Created on: 11.05.2011
5  * Author: mmann
6  */
7 
8 #ifndef NSPDK_PORT_HH_
9 #define NSPDK_PORT_HH_
10 
11 #include "sgm/Graph_Interface.hh"
12 #include "nspdk/GraphClass.h"
13 #include "nspdk/NSPDK_FeatureGenerator.h"
14 
15 
16 namespace sgm {
17 
18  /*! @brief Ports NSPDK functionality to SGM
19  *
20  * A utility class that ports the functionalities of the NSPDK graph kernel
21  * for its application the SGM library.
22  *
23  * @author Martin Mann (c) 2008 http://www.bioinf.uni-freiburg.de/~mmann/
24  */
25  class NSPDK_port {
26 
27  public:
28 
29  //! Sparse vector definition that represents the features of a graph
30  typedef nspdk::SVector FeatureVector;
31 
32  //! List of view points to localize the feature generation
33  typedef std::vector< unsigned > ViewPointList;
34 
35  protected:
36 
37  //! The standard NSPDK feature generator
38  static
39  nspdk::NSPDK_FeatureGenerator featureGenerator_nspdk;
40 
41  public:
42 
43  /*!
44  * Initializes an NSPDK graph object from a given Graph_Interface.
45  *
46  * @param iG IN the graph to be used for the initialization
47  * @param oG OUT the EMPTY graph object to be filled
48  *
49  */
50  static
51  void setGraphFromGraphInterface( const Graph_Interface & iG
52  , nspdk::GraphClass & oG);
53 
54  /*!
55  * Computes the feature vector for a given graph
56  *
57  * @param g IN the graph that has to be screened for features
58  * @param maxDistance the maximal distance between subgraphs to
59  * generate features
60  * @param maxRadius the maximal radius between subgraphs to
61  * generate features
62  * @param viewPoints IN optional list of view points to localize the
63  * feature generation to the according subgraph and its
64  * surrounding
65  * @param featureBitSize number of bits to represent the feature space
66  *
67  * @return the feature vector describing the graph g
68  */
69  static
70  FeatureVector
71  getFeatures( nspdk::GraphClass & g
72  , const size_t maxDistance
73  , const size_t maxRadius
74  , const ViewPointList & viewPoints = ViewPointList()
75  , const int featureBitSize = 30
76  );
77 
78 
79  /*!
80  * Computes the feature vector for each node of a given graph
81  *
82  * @param g IN the graph that has to be screened for features
83  * @param maxDistance the maximal distance between subgraphs to
84  * generate features
85  * @param maxRadius the maximal radius between subgraphs to
86  * generate features
87  * @param viewPoints IN optional list of view points to localize the
88  * feature generation to the according subgraph and its
89  * surrounding
90  * @param featureBitSize number of bits to represent the feature space
91  *
92  * @return the feature vector describing the graph g for each node
93  */
94  static
95  std::vector<NSPDK_port::FeatureVector>
96  getNodeFeatures( nspdk::GraphClass & g
97  , const size_t maxDistance
98  , const size_t maxRadius
99  , const ViewPointList & viewPoints = ViewPointList()
100  , const int featureBitSize = 30
101  );
102 
103 
104  };
105 
106 
107 } // namespace sgm
108 
109 
110 
111 #endif /* NSPDK_PORT_HH_ */