bpp-seq  2.2.0
SiteContainer.h
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1 //
2 // File SiteContainer.h
3 // Created by: Guillaume Deuchst
4 // Julien Dutheil
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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31  encouraged to load and test the software's suitability as regards their
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34  same conditions as regards security.
35 
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37  knowledge of the CeCILL license and that you accept its terms.
38  */
39 
40 #ifndef _SITECONTAINER_H_
41 #define _SITECONTAINER_H_
42 
43 #include "../Site.h"
46 #include <Bpp/Exceptions.h>
47 #include <Bpp/Numeric/VectorTools.h>
48 
49 // From the STL:
50 #include <string>
51 
52 namespace bpp
53 {
64  public virtual OrderedSequenceContainer
65 {
66 public:
68  virtual ~SiteContainer() {}
69 
70  SiteContainer* clone() const = 0;
71 
72 public:
80  virtual const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException) = 0;
81 
90  virtual void setSite(size_t siteIndex, const Site& site, bool checkPosition) throw (Exception) = 0;
91 
99  virtual void addSite(const Site& site, bool checkPosition) throw (Exception) = 0;
100 
109  virtual void addSite(const Site& site, int position, bool checkPosition) throw (Exception) = 0;
110 
119  virtual void addSite(const Site& site, size_t siteIndex, bool checkPosition) throw (Exception) = 0;
120 
130  virtual void addSite(const Site& site, size_t siteIndex, int position, bool checkPosition) throw (Exception) = 0;
131 
141  virtual Site* removeSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
142 
149  virtual void deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException, Exception) = 0;
150 
158  virtual void deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException, Exception) = 0;
159 
160 
166  virtual size_t getNumberOfSites() const = 0;
167 
171  virtual void reindexSites() = 0;
172 
178  virtual Vint getSitePositions() const = 0;
179 };
180 } // end of namespace bpp.
181 
182 #endif // _SITECONTAINER_H_
183 
virtual ~SiteContainer()
Definition: SiteContainer.h:68
The SiteContainer interface.
Definition: SiteContainer.h:63
The OrderedSequenceContainer interface.
This alphabet is used to deal NumericAlphabet.
virtual void setSite(size_t siteIndex, const Site &site, bool checkPosition)=0
Set a site in the container.
virtual void reindexSites()=0
Set all positions attributes.
virtual Site * removeSite(size_t siteIndex)=0
Remove a site from the container.
virtual void addSite(const Site &site, bool checkPosition)=0
Add a site in the container.
SiteContainer * clone() const =0
virtual const Site & getSite(size_t siteIndex) const =0
Get a site from the container.
virtual size_t getNumberOfSites() const =0
Get the number of sites in the container.
virtual Vint getSitePositions() const =0
Get all position attributes of sites.
The Site class.
Definition: Site.h:61
virtual void deleteSites(size_t siteIndex, size_t length)=0
Delete a continuous range of sites in the container.
virtual void deleteSite(size_t siteIndex)=0
Delete a site in the container.