bpp-seq3  3.0.0
AlignedValuesContainer.h
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1 //
2 // File: AlignedValuesContainer.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
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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_ALIGNEDVALUESCONTAINER_H
41 #define BPP_SEQ_CONTAINER_ALIGNEDVALUESCONTAINER_H
42 
43 #include <Bpp/Exceptions.h>
45 
46 #include "../CruxSymbolListSite.h"
47 #include "../Sequence.h"
48 #include "OrderedValuesContainer.h"
49 
50 // From the STL:
51 #include <string>
52 
53 namespace bpp
54 {
63  virtual public OrderedValuesContainer
64 {
65 public:
68 
70 
71 
78  virtual const CruxSymbolListSite& getSymbolListSite(size_t siteIndex) const = 0;
79 
80  virtual CruxSymbolListSite& getSymbolListSite(size_t siteIndex) = 0;
81 
89  virtual void deleteSites(size_t siteIndex, size_t length) = 0;
90 
97  virtual size_t getNumberOfSites() const = 0;
98 
103  virtual void reindexSites() = 0;
104 
111  virtual Vint getSitePositions() const = 0;
112 
119  virtual void setSitePositions(Vint vPositions) = 0;
120 };
121 } // end of namespace bpp.
122 #endif // BPP_SEQ_CONTAINER_ALIGNEDVALUESCONTAINER_H
The Container of Aligned Values interface.
virtual const CruxSymbolListSite & getSymbolListSite(size_t siteIndex) const =0
Get a CruxSymbolListSite from a given position.
virtual void setSitePositions(Vint vPositions)=0
Set all position attributes of sites.
AlignedValuesContainer * clone() const =0
virtual Vint getSitePositions() const =0
Get all position attributes of sites.
virtual void deleteSites(size_t siteIndex, size_t length)=0
Remove a continuous range of sites in the container.
virtual CruxSymbolListSite & getSymbolListSite(size_t siteIndex)=0
virtual void reindexSites()=0
Set all positions attributes.
virtual size_t getNumberOfSites() const =0
Get the number of aligned positions in the container.
The CruxSymbolListSite interface, from CoreSite and CruxSymbolList.
The Container of Ordered Values interface.
This alphabet is used to deal NumericAlphabet.
std::vector< int > Vint