bpp-seq3  3.0.0
OrderedValuesContainer.h
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1 //
2 // File: OrderedValuesContainer.h
3 // Authors:
4 // Laurent Guéguen
5 //
6 
7 /*
8  Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
9 
10  This software is a computer program whose purpose is to provide classes
11  for sequences analysis.
12 
13  This software is governed by the CeCILL license under French law and
14  abiding by the rules of distribution of free software. You can use,
15  modify and/ or redistribute the software under the terms of the CeCILL
16  license as circulated by CEA, CNRS and INRIA at the following URL
17  "http://www.cecill.info".
18 
19  As a counterpart to the access to the source code and rights to copy,
20  modify and redistribute granted by the license, users are provided only
21  with a limited warranty and the software's author, the holder of the
22  economic rights, and the successive licensors have only limited
23  liability.
24 
25  In this respect, the user's attention is drawn to the risks associated
26  with loading, using, modifying and/or developing or reproducing the
27  software by the user in light of its specific status of free software,
28  that may mean that it is complicated to manipulate, and that also
29  therefore means that it is reserved for developers and experienced
30  professionals having in-depth computer knowledge. Users are therefore
31  encouraged to load and test the software's suitability as regards their
32  requirements in conditions enabling the security of their systems and/or
33  data to be ensured and, more generally, to use and operate it in the
34  same conditions as regards security.
35 
36  The fact that you are presently reading this means that you have had
37  knowledge of the CeCILL license and that you accept its terms.
38 */
39 
40 #ifndef BPP_SEQ_CONTAINER_ORDEREDVALUESCONTAINER_H
41 #define BPP_SEQ_CONTAINER_ORDEREDVALUESCONTAINER_H
42 
43 #include <Bpp/Exceptions.h>
45 
47 
48 // From the STL:
49 #include <string>
50 
51 namespace bpp
52 {
63  virtual public SequencedValuesContainer
64 {
65 public:
68 
70 
80 
81  virtual std::string toString(size_t sequenceIndex) const = 0;
82 
92  virtual const std::string& getName(size_t sequenceIndex) const = 0;
93 
102  virtual size_t getSequencePosition(const std::string& name) const = 0;
103 
104  /*
105  * @brief get value of a state in a position
106  * @param siteIndex index of the site
107  * @param sequenceIndex index of the sequence in the container
108  * @param state state in the alphabet
109  */
110 
112 
113  virtual double getStateValueAt(size_t siteIndex, size_t sequenceIndex, int state) const = 0;
114 
115  virtual double operator()(size_t siteIndex, size_t sequenceIndex, int state) const = 0;
116 
127 
128  virtual const Comments& getComments(size_t sequenceIndex) const = 0;
129 
140 
141  virtual void setComments(size_t sequenceIndex, const Comments& comments) = 0;
142 };
143 } // end of namespace bpp.
144 #endif // BPP_SEQ_CONTAINER_ORDEREDVALUESCONTAINER_H
The Container of Ordered Values interface.
virtual double operator()(size_t siteIndex, size_t sequenceIndex, int state) const =0
virtual size_t getSequencePosition(const std::string &name) const =0
Get the position of a sequence in sequence container from its name.
virtual const std::string & getName(size_t sequenceIndex) const =0
Get the name of a particular row of the alignement (aka sequence).
virtual void setComments(size_t sequenceIndex, const Comments &comments)=0
virtual std::string toString(size_t sequenceIndex) const =0
virtual double getStateValueAt(size_t siteIndex, size_t sequenceIndex, int state) const =0
virtual const Comments & getComments(size_t sequenceIndex) const =0
OrderedValuesContainer * clone() const =0
virtual void setComments(const std::string &name, const Comments &comments)=0
Set the comments of a particular sequence.
virtual const Comments & getComments(const std::string &name) const =0
Get comments of a particular sequence.
virtual std::string toString(const std::string &name) const =0
Convert a particular sequence to a string.
virtual double getStateValueAt(size_t siteIndex, const std::string &sequenceName, int state) const =0
get value of a state in a position
This alphabet is used to deal NumericAlphabet.
std::vector< std::string > Comments
Declaration of Comments type.
Definition: Commentable.h:58