bpp-seq-omics  2.4.1
AlignmentFilterMafIterator.h
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1 //
2 // File: AlignmentFilterMafIterator.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
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17 "http://www.cecill.info".
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38 */
39 
40 #ifndef _ALIGNMENTFILTERMAFITERATOR_H_
41 #define _ALIGNMENTFILTERMAFITERATOR_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 
65  public virtual MafTrashIterator
66 {
67  private:
68  std::vector<std::string> species_;
69  unsigned int windowSize_;
70  unsigned int step_;
71  unsigned int maxGap_;
72  double maxPropGap_;
73  double maxEnt_;
74  std::deque<MafBlock*> blockBuffer_;
75  std::deque<MafBlock*> trashBuffer_;
76  std::deque< std::vector<int> > window_;
79  bool relative_;
80 
81  public:
82 
97  const std::vector<std::string>& species,
98  unsigned int windowSize,
99  unsigned int step,
100  unsigned int maxGap,
101  double maxEnt,
102  bool keepTrashedBlocks,
103  bool missingAsGap) :
104  AbstractFilterMafIterator(iterator),
105  species_(species),
106  windowSize_(windowSize),
107  step_(step),
108  maxGap_(maxGap),
109  maxPropGap_(),
110  maxEnt_(maxEnt),
111  blockBuffer_(),
112  trashBuffer_(),
113  window_(species.size()),
114  keepTrashedBlocks_(keepTrashedBlocks),
115  missingAsGap_(missingAsGap),
116  relative_(false)
117  {}
118 
133  const std::vector<std::string>& species,
134  unsigned int windowSize,
135  unsigned int step,
136  double maxPropGap,
137  double maxEnt,
138  bool keepTrashedBlocks,
139  bool missingAsGap) :
140  AbstractFilterMafIterator(iterator),
141  species_(species),
142  windowSize_(windowSize),
143  step_(step),
144  maxGap_(),
145  maxPropGap_(maxPropGap),
146  maxEnt_(maxEnt),
147  blockBuffer_(),
148  trashBuffer_(),
149  window_(species.size()),
150  keepTrashedBlocks_(keepTrashedBlocks),
151  missingAsGap_(missingAsGap),
152  relative_(true)
153  {}
154 
155 
156  public:
158  if (trashBuffer_.size() == 0) return 0;
159  MafBlock* block = trashBuffer_.front();
160  trashBuffer_.pop_front();
161  return block;
162  }
163 
164  private:
166 };
167 
178  public virtual MafTrashIterator
179 {
180  private:
181  std::vector<std::string> species_;
182  unsigned int windowSize_;
183  unsigned int step_;
184  unsigned int maxGap_;
185  double maxPropGap_;
186  unsigned int maxPos_;
187  std::deque<MafBlock*> blockBuffer_;
188  std::deque<MafBlock*> trashBuffer_;
189  std::deque< std::vector<bool> > window_;
192  bool relative_;
193 
194  public:
208  AlignmentFilter2MafIterator(MafIterator* iterator, const std::vector<std::string>& species, unsigned int windowSize, unsigned int step, unsigned int maxGap, unsigned int maxPos, bool keepTrashedBlocks, bool missingAsGap) :
209  AbstractFilterMafIterator(iterator),
210  species_(species),
211  windowSize_(windowSize),
212  step_(step),
213  maxGap_(maxGap),
214  maxPropGap_(),
215  maxPos_(maxPos),
216  blockBuffer_(),
217  trashBuffer_(),
218  window_(species.size()),
219  keepTrashedBlocks_(keepTrashedBlocks),
220  missingAsGap_(missingAsGap),
221  relative_(false)
222  {}
223 
237  AlignmentFilter2MafIterator(MafIterator* iterator, const std::vector<std::string>& species, unsigned int windowSize, unsigned int step, double maxPropGap, unsigned int maxPos, bool keepTrashedBlocks, bool missingAsGap) :
238  AbstractFilterMafIterator(iterator),
239  species_(species),
240  windowSize_(windowSize),
241  step_(step),
242  maxGap_(),
243  maxPropGap_(maxPropGap),
244  maxPos_(maxPos),
245  blockBuffer_(),
246  trashBuffer_(),
247  window_(species.size()),
248  keepTrashedBlocks_(keepTrashedBlocks),
249  missingAsGap_(missingAsGap),
250  relative_(true)
251  {}
252 
253  public:
255  if (trashBuffer_.size() == 0) return 0;
256  MafBlock* block = trashBuffer_.front();
257  trashBuffer_.pop_front();
258  return block;
259  }
260 
261  private:
263 
264 };
265 
266 } // end of namespace bpp.
267 
268 #endif //_ALIGNMENTFILTERMAFITERATOR_H_
Helper class for developping filter for maf blocks.
Definition: MafIterator.h:151
Filter maf blocks to remove ambiguously aligned or non-informative regions.
AlignmentFilter2MafIterator(MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, unsigned int maxGap, unsigned int maxPos, bool keepTrashedBlocks, bool missingAsGap)
Create a new AlignmentFilter2MafIterator with absolute thresholds.
std::deque< std::vector< bool > > window_
AlignmentFilter2MafIterator(MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, double maxPropGap, unsigned int maxPos, bool keepTrashedBlocks, bool missingAsGap)
Create a new AlignmentFilterMafIterator with relative thresholds.
MafBlock * nextRemovedBlock()
Get the next available removed alignment block.
Filter maf blocks to remove ambiguously aligned or non-informative regions.
AlignmentFilterMafIterator(MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, unsigned int maxGap, double maxEnt, bool keepTrashedBlocks, bool missingAsGap)
Create a new AlignmentFilterMafIterator with absolute thresholds.
std::deque< std::vector< int > > window_
AlignmentFilterMafIterator(MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, double maxPropGap, double maxEnt, bool keepTrashedBlocks, bool missingAsGap)
Create a new AlignmentFilterMafIterator with relative thresholds.
MafBlock * nextRemovedBlock()
Get the next available removed alignment block.
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