bpp-seq  2.2.0
SequenceWithQualityTools.h
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1 //
2 // File: SequenceWithQualityTools.h
3 // Authors: Vincent Cahais
4 // Sylvain Gaillard
5 // Created on: 16 Apr 2010
6 //
7 
8 /*
9 Copyright or © or Copr. Bio++ Development Team, (Apr 16, 2010)
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 SEQUENCEWITHQUALITYTOOLS_H_
42 #define SEQUENCEWITHQUALITYTOOLS_H_
43 
44 #include "SequenceTools.h"
45 #include "SequenceWithQuality.h"
46 
47 namespace bpp {
61  private:
62  static DNA _DNA;
63  static RNA _RNA;
67 
68  public:
69 
80  const SequenceWithQuality& sequence,
81  unsigned int begin,
82  unsigned int end
83  ) throw (IndexOutOfBoundsException, Exception) ;
84 
99  const SequenceWithQuality& seqwq1,
100  const SequenceWithQuality& seqwq2
101  ) throw (AlphabetMismatchException, Exception) ;
102 
113  const SequenceWithQuality& sequence
114  ) throw (AlphabetException);
115 
126  const SequenceWithQuality& sequence
127  ) throw (AlphabetException);
128 
140  const SequenceWithQuality& sequence
141  ) throw (AlphabetException);
152  static SequenceWithQuality* invert(
153  const SequenceWithQuality& sequence
154  );
155 
163 
171 
172  };
173 }
174 
175 #endif /* SEQUENCEWITHQUALITYTOOLS_H_ */
static SequenceWithQuality * invert(const SequenceWithQuality &sequence)
Inverse a sequence from 5'->3' to 3'->5' and vice-versa.
static SequenceWithQuality * reverseTranscript(const SequenceWithQuality &sequence)
Get the reverse-transcription sequence of a RNA sequence.
This alphabet is used to deal NumericAlphabet.
static SequenceWithQuality * removeGaps(const SequenceWithQuality &seq)
Remove gaps from a SequenceWithQuality.
static SequenceWithQuality & trimLeft(SequenceWithQuality &seq)
Trim the left part of the sequence according to quality.
A SequenceWithAnnotation class with quality scores attached.
The SequenceWithQualityTools static class.
static NucleicAcidsReplication _transc
static SequenceWithQuality * complement(const SequenceWithQuality &sequence)
Get the complementary sequence of a nucleotide sequence.
static SequenceWithQuality * concatenate(const SequenceWithQuality &seqwq1, const SequenceWithQuality &seqwq2)
Concatenate two sequences.
static SequenceWithQuality * transcript(const SequenceWithQuality &sequence)
Get the transcription sequence of a DNA sequence.
static SequenceWithQuality * subseq(const SequenceWithQuality &sequence, unsigned int begin, unsigned int end)
Get a sub-sequence.
The alphabet exception base class.
static NucleicAcidsReplication _RNARep
This alphabet is used to deal with DNA sequences.
Definition: DNA.h:60
static NucleicAcidsReplication _DNARep
This alphabet is used to deal with RNA sequences.
Definition: RNA.h:58
Exception thrown when two alphabets do not match.
Replication between to nucleic acids.