bpp-seq-omics  2.4.1
MsmcOutputMafIterator.h
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1 //
2 // File: MsmcOutputMafIterator.h
3 // Authors: Julien Dutheil
4 // Created: Tue Jan 06 2015
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (2015)
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 
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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
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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,
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38 */
39 
40 #ifndef _MSMCOUTPUTMAFITERATOR_H_
41 #define _MSMCOUTPUTMAFITERATOR_H_
42 
43 #include "MafIterator.h"
44 
45 //From the STL:
46 #include <iostream>
47 #include <string>
48 #include <deque>
49 
50 namespace bpp {
51 
59 {
60  private:
61  std::ostream* output_;
62  std::vector<std::string> species_;
63  std::string refSpecies_;
64  std::string currentChr_;
65  size_t lastPosition_;
66  unsigned int nbOfCalledSites_;
67 
68  public:
81  std::ostream* out,
82  const std::vector<std::string>& species,
83  const std::string& reference) :
84  AbstractFilterMafIterator(iterator),
85  output_(out), species_(species), refSpecies_(reference),
87  {}
88 
89  private:
92  output_(iterator.output_),
93  species_(iterator.species_),
94  refSpecies_(iterator.refSpecies_),
95  currentChr_(iterator.currentChr_),
96  lastPosition_(iterator.lastPosition_),
98  {}
99 
101  {
102  output_ = iterator.output_;
103  species_ = iterator.species_;
104  refSpecies_ = iterator.refSpecies_;
105  currentChr_ = iterator.currentChr_;
106  lastPosition_ = iterator.lastPosition_;
108  return *this;
109  }
110 
111 
112  public:
115  if (output_ && currentBlock_)
117  return currentBlock_;
118  }
119 
120  private:
121  void writeBlock_(std::ostream& out, const MafBlock& block);
122 };
123 
124 } // end of namespace bpp.
125 
126 #endif //_MSMCOUTPUTMAFITERATOR_H_
Helper class for developping filter for maf blocks.
Definition: MafIterator.h:151
A synteny block data structure, the basic unit of a MAF alignement file.
Definition: MafBlock.h:57
Interface to loop over maf alignment blocks.
Definition: MafIterator.h:59
virtual MafBlock * nextBlock()=0
Get the next available alignment block.
This iterator outputs all SNPs in the format readable by MSMC.
MsmcOutputMafIterator(MafIterator *iterator, std::ostream *out, const std::vector< std::string > &species, const std::string &reference)
Build a new MsmcOutputMafIterator object.
std::vector< std::string > species_
MsmcOutputMafIterator & operator=(const MsmcOutputMafIterator &iterator)
void writeBlock_(std::ostream &out, const MafBlock &block)
MsmcOutputMafIterator(const MsmcOutputMafIterator &iterator)