bpp-seq  2.2.0
PhredPhd.h
Go to the documentation of this file.
1 //
2 // File: PhredPhd.h
3 // Created by: Sylvain Gaillard
4 // Created on: Wed Nov 5 2008
5 //
6 
7 /*
8 Copyright or © or Copr. CNRS, (November 5, 2008)
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 _PHREDPHD_H_
41 #define _PHREDPHD_H_
42 
43 #include "ISequenceStream.h"
44 #include "../Sequence.h"
45 #include "../SequenceWithQuality.h"
46 
47 namespace bpp {
48 
78  class PhredPhd: public ISequenceStream {
79  public:
80 
84  PhredPhd() {}
85 
86  virtual ~PhredPhd() {}
87 
88  public:
94  bool nextSequence(
95  std::istream& input,
96  Sequence& seq
97  ) const throw (Exception);
112  bool nextSequence(
113  std::istream& input,
114  Sequence& seq,
115  std::vector<int>& pos
116  ) const throw (Exception);
117 
123  const std::string getDataType() const { return "SequenceWithQuality"; };
124  const std::string getFormatName() const { return "phd file"; };
125  const std::string getFormatDescription() const {
126  return "Sequences following the phd format as describe in the phred documentation.";
127  }
130  private:
140  bool parseFile_(std::istream& input, std::string& name, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos) const;
141 
152  bool parseDNA_(std::istream& input, std::string& sequence, std::vector<int>& qual, std::vector<int>& pos) const;
153  };
154 } //end of namespace bpp
155 
156 #endif // _PHREDPHD_H_
PhredPhd()
Build a new PhredPhd object.
Definition: PhredPhd.h:84
This alphabet is used to deal NumericAlphabet.
The phd sequence file format from phred software.
Definition: PhredPhd.h:78
virtual ~PhredPhd()
Definition: PhredPhd.h:86
bool nextSequence(std::istream &input, Sequence &seq) const
Read sequence from stream.
Definition: PhredPhd.cpp:52
const std::string getFormatDescription() const
Definition: PhredPhd.h:125
const std::string getDataType() const
Definition: PhredPhd.h:123
bool parseFile_(std::istream &input, std::string &name, std::string &sequence, std::vector< int > &qual, std::vector< int > &pos) const
Global file parser.
Definition: PhredPhd.cpp:84
The sequence interface.
Definition: Sequence.h:74
The ISequenceStream interface.
bool parseDNA_(std::istream &input, std::string &sequence, std::vector< int > &qual, std::vector< int > &pos) const
Parse the DNA part of the file.
Definition: PhredPhd.cpp:115
const std::string getFormatName() const
Definition: PhredPhd.h:124