bpp-seq-omics  2.4.1
MafParser.h
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1 //
2 // File: MafParser.h
3 // Authors: Julien Dutheil
4 // Created: Tue Apr 27 2010
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (2010)
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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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 _MAFPARSER_H_
41 #define _MAFPARSER_H_
42 
43 #include "MafIterator.h"
45 
46 //From the STL:
47 #include <iostream>
48 
49 namespace bpp {
50 
61 class MafParser:
62  public AbstractMafIterator
63 {
64  private:
65  std::istream* stream_;
66  bool mask_;
70  short dotOption_;
71 
72  public:
88  MafParser(std::istream* stream, bool parseMask = false, bool checkSize = true, short dotOption = DOT_ERROR) :
89  stream_(stream), mask_(parseMask), checkSequenceSize_(checkSize), cmAlphabet_(&AlphabetTools::DNA_ALPHABET),
90  firstBlock_(true), dotOption_(dotOption) {}
91 
92  private:
93  //Recopy is forbidden!
94  MafParser(const MafParser& maf):
96  cmAlphabet_(&AlphabetTools::DNA_ALPHABET), firstBlock_(maf.firstBlock_),
97  dotOption_(maf.dotOption_) {}
98 
99  MafParser& operator=(const MafParser& maf) {
100  stream_ = 0;
101  mask_ = maf.mask_;
103  firstBlock_ = maf.firstBlock_;
104  dotOption_ = maf.dotOption_;
105  return *this;
106  }
107 
108  private:
110 
111  public:
112  static constexpr short DOT_ERROR = 0;
113  static constexpr short DOT_ASGAP = 1;
114  static constexpr short DOT_ASUNRES = 2;
115  //static constexpr short DOT_RESOLVE = 3; // not yet supported
116 
117 };
118 
119 } // end of namespace bpp.
120 
121 #endif //_MAFPARSER_H_
122 
Partial implementation of the MafIterator interface.
Definition: MafIterator.h:87
A synteny block data structure, the basic unit of a MAF alignement file.
Definition: MafBlock.h:57
MAF file parser.
Definition: MafParser.h:63
static constexpr short DOT_ERROR
Definition: MafParser.h:112
short dotOption_
Definition: MafParser.h:70
MafParser & operator=(const MafParser &maf)
Definition: MafParser.h:99
bool firstBlock_
Definition: MafParser.h:69
bool checkSequenceSize_
Definition: MafParser.h:67
MafParser(const MafParser &maf)
Definition: MafParser.h:94
std::istream * stream_
Definition: MafParser.h:65
CaseMaskedAlphabet cmAlphabet_
Definition: MafParser.h:68
static constexpr short DOT_ASGAP
Definition: MafParser.h:113
MafBlock * analyseCurrentBlock_()
Definition: MafParser.cpp:51
static constexpr short DOT_ASUNRES
Definition: MafParser.h:114
MafParser(std::istream *stream, bool parseMask=false, bool checkSize=true, short dotOption=DOT_ERROR)
Create a new instance of MafParser.
Definition: MafParser.h:88