bpp-phyl  2.4.0
TreeLikelihoodData.h
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1 //
2 // File: TreeLikelihoodData.h
3 // Created by: Julien Dutheil
4 // Created on: Sat Dec 30 12:48 2006
5 // From file AbstractTreeLikelihood.h
6 //
7 
8 /*
9 Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
10 
11 This software is a computer program whose purpose is to provide classes
12 for phylogenetic data analysis.
13 
14 This software is governed by the CeCILL license under French law and
15 abiding by the rules of distribution of free software. You can use,
16 modify and/ or redistribute the software under the terms of the CeCILL
17 license as circulated by CEA, CNRS and INRIA at the following URL
18 "http://www.cecill.info".
19 
20 As a counterpart to the access to the source code and rights to copy,
21 modify and redistribute granted by the license, users are provided only
22 with a limited warranty and the software's author, the holder of the
23 economic rights, and the successive licensors have only limited
24 liability.
25 
26 In this respect, the user's attention is drawn to the risks associated
27 with loading, using, modifying and/or developing or reproducing the
28 software by the user in light of its specific status of free software,
29 that may mean that it is complicated to manipulate, and that also
30 therefore means that it is reserved for developers and experienced
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35 same conditions as regards security.
36 
37 The fact that you are presently reading this means that you have had
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39 */
40 
41 #ifndef _TREELIKELIHOODDATA_H_
42 #define _TREELIKELIHOODDATA_H_
43 
44 #include "../Node.h"
45 #include "../TreeTemplate.h"
46 
47 //From SeqLib:
50 
51 namespace bpp
52 {
53 
62  public virtual Clonable
63 {
64  public:
67 
68  TreeLikelihoodNodeData* clone() const = 0;
69 
70  public:
76  virtual const Node* getNode() const = 0;
77 
85  virtual void setNode(const Node* node) = 0;
86 };
87 
98  public virtual Clonable
99 {
100  public:
102  virtual ~TreeLikelihoodData() {}
103 
104  TreeLikelihoodData* clone() const = 0;
105 
106  public:
107  virtual const Alphabet* getAlphabet() const = 0;
108  virtual const TreeTemplate<Node>* getTree() const = 0;
109  virtual size_t getArrayPosition(int parentId, int sonId, size_t currentPosition) const = 0;
110  virtual size_t getRootArrayPosition(size_t site) const = 0;
111  virtual TreeLikelihoodNodeData& getNodeData(int nodeId) = 0;
112  virtual const TreeLikelihoodNodeData& getNodeData(int nodeId) const = 0;
113 
117  virtual size_t getNumberOfDistinctSites() const = 0;
118 
122  virtual size_t getNumberOfSites() const = 0;
123 
127  virtual size_t getNumberOfStates() const = 0;
128 
132  virtual unsigned int getWeight(size_t pos) const = 0;
133 
137  virtual const std::vector<unsigned int>& getWeights() const = 0;
138 
139 };
140 
141 } //end of namespace bpp.
142 
143 #endif //_TREELIKELIHOODDATA_H_
144 
virtual void setNode(const Node *node)=0
Set the node associated to this data.
TreeLikelihood data structure.
The phylogenetic tree class.
virtual const Node * getNode() const =0
Get the node associated to this data structure.
TreeLikelihoodNodeData * clone() const =0
The phylogenetic node class.
Definition: Node.h:90
TreeLikelihood partial data structure.