bpp-seq-omics  2.4.1
FeatureExtractorMafIterator.h
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1 //
2 // File: FeatureExtractorMafIterator.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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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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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 _FEATUREEXTRACTORMAFITERATOR_H_
41 #define _FEATUREEXTRACTORMAFITERATOR_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:
64  std::string refSpecies_;
67  std::deque<MafBlock*> blockBuffer_;
68  std::map<std::string, RangeSet<size_t> > ranges_;
69 
70  public:
80  FeatureExtractorMafIterator(MafIterator* iterator, const std::string& refSpecies, const SequenceFeatureSet& features, bool complete = false, bool ignoreStrand = false) :
81  AbstractFilterMafIterator(iterator),
82  refSpecies_(refSpecies),
83  completeOnly_(complete),
84  ignoreStrand_(ignoreStrand),
85  blockBuffer_(),
86  ranges_()
87  {
88  //Build ranges:
89  std::set<std::string> seqIds = features.getSequences();
90  for (std::set<std::string>::iterator it = seqIds.begin();
91  it != seqIds.end();
92  ++it) {
93  {
94  features.fillRangeCollectionForSequence(*it, ranges_[*it]);
95  }
96  }
97  }
98 
99  private:
101 
102 };
103 
104 } // end of namespace bpp.
105 
106 #endif //_FEATUREEXTRACTORMAFITERATOR_H_
Helper class for developping filter for maf blocks.
Definition: MafIterator.h:151
Extract alignments corresponding to sequence features given as a vector of SequenceFeature objects.
FeatureExtractorMafIterator(MafIterator *iterator, const std::string &refSpecies, const SequenceFeatureSet &features, bool complete=false, bool ignoreStrand=false)
Build a new FeatureExtractor iterator.
std::map< std::string, RangeSet< size_t > > ranges_
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
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