bpp-seq  2.2.0
OrderedSequenceContainer.h
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1 //
2 // File OrderedSequenceContainer.h
3 // Author: Guillaume Deuchst
4 // Julien Dutheil
5 // Last modification : Tuesday August 7 2003
6 //
7 
8 /*
9 Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
10 
11 This software is a computer program whose purpose is to provide classes
12 for sequences 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
31 professionals having in-depth computer knowledge. Users are therefore
32 encouraged to load and test the software's suitability as regards their
33 requirements in conditions enabling the security of their systems and/or
34 data to be ensured and, more generally, to use and operate it in the
35 same conditions as regards security.
36 
37 The fact that you are presently reading this means that you have had
38 knowledge of the CeCILL license and that you accept its terms.
39 */
40 
41 #ifndef _ORDEREDSEQUENCECONTAINER_H_
42 #define _ORDEREDSEQUENCECONTAINER_H_
43 
44 #include "../Sequence.h"
45 #include "SequenceContainer.h"
46 
47 namespace bpp
48 {
49 
57  public virtual SequenceContainer
58 {
59  public:
62 
63  public:
71  virtual const std::vector<int>& getContent(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
72 
80  virtual std::string toString(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
81 
90  virtual const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
91 
102  virtual void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception) = 0;
103 
111  virtual Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
112 
120  virtual void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, Exception) = 0;
121 
130  virtual const std::string& getName(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
131 
140  virtual const Comments& getComments(size_t sequenceIndex) const throw (IndexOutOfBoundsException) = 0;
141 
150  virtual void setComments(size_t sequenceIndex, const Comments & comments) throw (IndexOutOfBoundsException) = 0;
151 
159  virtual size_t getSequencePosition(const std::string & name) const throw (SequenceNotFoundException) = 0;
160 
171  virtual int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
172 
173  virtual const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException) = 0;
174 
184  virtual int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException) = 0;
185 
195  virtual const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException) = 0;
196 
207  virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0;
208 
219  virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0;
222  public:
223 
229  virtual const std::vector<int>& getContent(const std::string& name) const throw (SequenceNotFoundException) = 0;
230  virtual std::string toString(const std::string& name) const throw (SequenceNotFoundException) = 0;
231  virtual const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException) = 0;
232  virtual void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception) = 0;
233  virtual Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
234  virtual void deleteSequence(const std::string& name) throw (SequenceNotFoundException, Exception) = 0;
235  virtual size_t getNumberOfSequences() const = 0;
236  virtual std::vector<std::string> getSequencesNames() const = 0;
237  virtual void setSequencesNames(const std::vector<std::string> & names, bool checkNames) throw (Exception) = 0;
238  virtual const Comments& getComments(const std::string& name) const throw (SequenceNotFoundException) = 0;
239  virtual void setComments(const std::string& name, const Comments& comments) throw (SequenceNotFoundException) = 0;
241 };
242 
243 } //end of namespace bpp.
244 
245 #endif //_ORDEREDSEQUENCECONTAINER_H_
246 
virtual void setComments(size_t sequenceIndex, const Comments &comments)=0
Set the comments of a particular sequence.
virtual int & operator()(size_t sequenceIndex, size_t elementIndex)=0
Element access operator.
Exception thrown when a sequence is not found The sequence not found exception base class...
std::vector< std::string > Comments
Declaration of Comments type.
Definition: Sequence.h:60
virtual const std::vector< int > & getContent(size_t sequenceIndex) const =0
Get the content of a sequence.
virtual void deleteSequence(size_t sequenceIndex)=0
Delete a sequence of the container.
The OrderedSequenceContainer interface.
This alphabet is used to deal NumericAlphabet.
virtual void setSequence(size_t sequenceIndex, const Sequence &sequence, bool checkName)=0
Replace a sequence in the container.
virtual const Comments & getComments(size_t sequenceIndex) const =0
Get comments of a particular sequence.
virtual const Sequence & getSequence(size_t sequenceIndex) const =0
Retrieve a sequence object from the container.
virtual int & valueAt(const std::string &sequenceName, size_t elementIndex)=0
Element access function.
virtual void setSequencesNames(const std::vector< std::string > &names, bool checkNames)=0
Set all sequence names.
virtual std::string toString(size_t sequenceIndex) const =0
Convert a particular sequence to a string.
virtual size_t getSequencePosition(const std::string &name) const =0
Get the position of a sequence in sequence container from its name.
virtual Sequence * removeSequence(size_t sequenceIndex)=0
Extract (and remove) a sequence from the container.
virtual const std::string & getName(size_t sequenceIndex) const =0
Get the name of a particular sequence.
The sequence interface.
Definition: Sequence.h:74
virtual std::vector< std::string > getSequencesNames() const =0
Get all the names of the sequences in the container.
The SequenceContainer interface.
virtual size_t getNumberOfSequences() const =0
Get the number of sequences in the container.