bpp-seq-omics  2.4.1
FeatureFilterMafIterator.h
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1 //
2 // File: FeatureFilterMafIterator.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,
28 that may mean that it is complicated to manipulate, and that also
29 therefore means that it is reserved for developers and experienced
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34 same conditions as regards security.
35 
36 The fact that you are presently reading this means that you have had
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38 */
39 
40 #ifndef _FEATUREFILTERMAFITERATOR_H_
41 #define _FEATUREFILTERMAFITERATOR_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  public MafTrashIterator
60 {
61  private:
62  std::string refSpecies_;
63  std::deque<MafBlock*> blockBuffer_;
64  std::deque<MafBlock*> trashBuffer_;
66  std::map<std::string, MultiRange<size_t> > ranges_;
67 
68  public:
69  FeatureFilterMafIterator(MafIterator* iterator, const std::string& refSpecies, const SequenceFeatureSet& features, bool keepTrashedBlocks) :
70  AbstractFilterMafIterator(iterator),
71  refSpecies_(refSpecies),
72  blockBuffer_(),
73  trashBuffer_(),
74  keepTrashedBlocks_(keepTrashedBlocks),
75  ranges_()
76  {
77  //Build ranges:
78  std::set<std::string> seqIds = features.getSequences();
79  for (std::set<std::string>::iterator it = seqIds.begin();
80  it != seqIds.end();
81  ++it) {
82  {
83  features.fillRangeCollectionForSequence(*it, ranges_[*it]);
84  }
85  }
86  }
87 
88  public:
90  if (trashBuffer_.size() == 0) return 0;
91  MafBlock* block = trashBuffer_.front();
92  trashBuffer_.pop_front();
93  return block;
94  }
95 
96  private:
98 
99 };
100 
101 } // end of namespace bpp.
102 
103 #endif //_FEATUREFILTERMAFITERATOR_H_
Helper class for developping filter for maf blocks.
Definition: MafIterator.h:151
Remove from alignment all positions that fall within any feature from a list given as a SequenceFeatu...
std::map< std::string, MultiRange< size_t > > ranges_
std::deque< MafBlock * > blockBuffer_
FeatureFilterMafIterator(MafIterator *iterator, const std::string &refSpecies, const SequenceFeatureSet &features, bool keepTrashedBlocks)
MafBlock * nextRemovedBlock()
Get the next available removed alignment block.
std::deque< MafBlock * > trashBuffer_
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
A simple ensemble of sequence features.
void fillRangeCollectionForSequence(const std::string &seqId, RangeCollection< size_t > &coords) const
Get all coordinates of features for a given source. All ranges are added to a RangeCollection contain...
std::set< std::string > getSequences() const