bpp-seq-omics  2.4.1
DuplicateFilterMafIterator.h
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1 //
2 // File: DuplicateFilterMafIterator.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".
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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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,
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38 */
39 
40 #ifndef _DUPLICATEFILTERMAFITERATOR_H_
41 #define _DUPLICATEFILTERMAFITERATOR_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 
57 {
58  private:
59  std::string ref_;
63  std::map< std::string, std::map< char, std::map< size_t, std::map< size_t, size_t > > > > blocks_;
64 
65  public:
70  DuplicateFilterMafIterator(MafIterator* iterator, const std::string& reference) :
71  AbstractFilterMafIterator(iterator),
72  ref_(reference),
73  blocks_()
74  {}
75 
76  private:
79  ref_(iterator.ref_),
80  blocks_(iterator.blocks_)
81  {}
82 
84  {
85  ref_ = iterator.ref_;
86  blocks_ = iterator.blocks_;
87  return *this;
88  }
89 
90  private:
92 
93 };
94 
95 } // end of namespace bpp.
96 
97 #endif //_DUPLICATEFILTERMAFITERATOR_H_
Helper class for developping filter for maf blocks.
Definition: MafIterator.h:151
Filter maf blocks to remove duplicated blocks, according to a reference sequence).
DuplicateFilterMafIterator(const DuplicateFilterMafIterator &iterator)
DuplicateFilterMafIterator & operator=(const DuplicateFilterMafIterator &iterator)
DuplicateFilterMafIterator(MafIterator *iterator, const std::string &reference)
std::map< std::string, std::map< char, std::map< size_t, std::map< size_t, size_t > > > > blocks_
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