bpp-seq  2.2.0
SequenceExceptions.h
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1 //
2 // File: SequenceExceptions.h
3 // Created by: Julien Dutheil
4 // Created on: Mon Nov 3 16:35:30 2003
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 _SEQUENCEEXCEPTIONS_H_
41 #define _SEQUENCEEXCEPTIONS_H_
42 
43 #include "Alphabet/Alphabet.h"
44 #include <Bpp/Exceptions.h>
45 
46 namespace bpp
47 {
48 
49 class Sequence;
50 
57  public Exception
58 {
59  private:
60 
65 
66  public:
67 
74  SequenceException(const std::string& text, const Sequence * seq = 0);
75 
76  SequenceException(const SequenceException& se): Exception(se), sequence_(se.sequence_) {}
78  {
79  Exception::operator=(se);
80  sequence_ = se.sequence_;
81  return *this;
82  }
83 
84  virtual ~SequenceException() throw() {}
85 
86  public:
87 
93  virtual const Sequence* getSequence() const { return sequence_; }
94 };
95 
100  public SequenceException
101 {
102 
103  public:
104 
111  EmptySequenceException(const std::string& text, const Sequence* seq = 0);
112 
113  virtual ~EmptySequenceException() throw() {}
114 };
115 
120  public SequenceException
121 {
122 
123  public:
124 
131  SequenceWithGapException(const std::string& text, const Sequence* seq = 0);
132 
133  virtual ~SequenceWithGapException() throw() {}
134 };
135 
142  public SequenceException
143 {
144 
145  public:
146 
153  SequenceNotAlignedException(const std::string& text, const Sequence* seq);
154 
155  virtual ~SequenceNotAlignedException() throw() {}
156 };
157 
158 } //end of namespace bpp.
159 
160 #endif //_SEQUENCEEXCEPTIONS_H_
161 
SequenceException(const std::string &text, const Sequence *seq=0)
Build a new SequenceException object.
SequenceWithGapException(const std::string &text, const Sequence *seq=0)
Build a new SequenceWithGapException object.
SequenceException(const SequenceException &se)
SequenceException & operator=(const SequenceException &se)
This alphabet is used to deal NumericAlphabet.
Exception thrown when a sequence is found to have gap and it should not.
SequenceNotAlignedException(const std::string &text, const Sequence *seq)
Build a new SequenceNotAlignedException object.
virtual const Sequence * getSequence() const
Get the sequence that threw the exception.
EmptySequenceException(const std::string &text, const Sequence *seq=0)
Build a new EmptySequenceException object.
const Sequence * sequence_
A pointer toward a sequence object.
The sequence exception base class.
The sequence interface.
Definition: Sequence.h:74
Exception thrown when a sequence is found to be empty and it should not.
Exception thrown when a sequence is not align with others.