bpp-seq-omics  2.4.1
ConcatenateMafIterator.h
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1 //
2 // File: ConcatenateMafIterator.h
3 // Authors: Julien Dutheil
4 // Created: Tue Sep 07 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".
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38 */
39 
40 #ifndef _CONCATENATEMAFITERATOR_H_
41 #define _CONCATENATEMAFITERATOR_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 
62 {
63  private:
65  unsigned int minimumSize_;
66  std::string refSpecies_;
67 
68  public:
69  ConcatenateMafIterator(MafIterator* iterator, unsigned int minimumSize, std::string refSpecies = "") :
70  AbstractFilterMafIterator(iterator),
71  incomingBlock_(0),
72  minimumSize_(minimumSize),
73  refSpecies_(refSpecies)
74  {
75  incomingBlock_ = iterator->nextBlock();
76  }
77 
78  private:
82  minimumSize_(iterator.minimumSize_),
83  refSpecies_(iterator.refSpecies_)
84  {}
85 
87  {
88  incomingBlock_ = iterator.incomingBlock_;
89  minimumSize_ = iterator.minimumSize_;
90  refSpecies_ = iterator.refSpecies_;
91  return *this;
92  }
93 
94  private:
96 
97 };
98 
99 } // end of namespace bpp.
100 
101 #endif //_CONCATENATEMAFITERATOR_H_
Helper class for developping filter for maf blocks.
Definition: MafIterator.h:151
Concatenate blocks up to a certain size.
ConcatenateMafIterator(MafIterator *iterator, unsigned int minimumSize, std::string refSpecies="")
ConcatenateMafIterator(const ConcatenateMafIterator &iterator)
ConcatenateMafIterator & operator=(const ConcatenateMafIterator &iterator)
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.