bpp-seq-omics  2.4.1
MaskFilterMafIterator.h
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1 //
2 // File: MaskFilterMafIterator.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 
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,
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34 same conditions as regards security.
35 
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38 */
39 
40 #ifndef _MASKFILTERMAFITERATOR_H_
41 #define _MASKFILTERMAFITERATOR_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 
60  public MafTrashIterator
61 {
62  private:
63  std::vector<std::string> species_;
64  unsigned int windowSize_;
65  unsigned int step_;
66  unsigned int maxMasked_;
67  std::deque<MafBlock*> blockBuffer_;
68  std::deque<MafBlock*> trashBuffer_;
69  std::deque< std::vector<bool> > window_;
71 
72  public:
73  MaskFilterMafIterator(MafIterator* iterator, const std::vector<std::string>& species, unsigned int windowSize, unsigned int step, unsigned int maxMasked, bool keepTrashedBlocks) :
74  AbstractFilterMafIterator(iterator),
75  species_(species),
76  windowSize_(windowSize),
77  step_(step),
78  maxMasked_(maxMasked),
79  blockBuffer_(),
80  trashBuffer_(),
81  window_(species.size()),
82  keepTrashedBlocks_(keepTrashedBlocks)
83  {}
84 
85  public:
87  if (trashBuffer_.size() == 0) return 0;
88  MafBlock* block = trashBuffer_.front();
89  trashBuffer_.pop_front();
90  return block;
91  }
92 
93  private:
95 
96 };
97 
98 } // end of namespace bpp.
99 
100 #endif //_MASKFILTERMAFITERATOR_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
Interface to loop over removed blocks of a maf alignment.
Definition: MafIterator.h:131
Filter maf blocks to remove regions with masked positions.
MafBlock * nextRemovedBlock()
Get the next available removed alignment block.
std::vector< std::string > species_
std::deque< std::vector< bool > > window_
std::deque< MafBlock * > trashBuffer_
MaskFilterMafIterator(MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, unsigned int maxMasked, bool keepTrashedBlocks)
std::deque< MafBlock * > blockBuffer_