bpp-seq-omics  2.4.1
CoordinateTranslatorMafIterator.h
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1 //
2 // File: CoordinateTranslatorMafIterator.h
3 // Authors: Julien Dutheil
4 // Created: Thu Jan 28 2016
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 _COORDINATETRANSLATORMAFITERATOR_H_
41 #define _COORDINATETRANSLATORMAFITERATOR_H_
42 
43 #include "MafIterator.h"
44 
45 //From the STL:
46 #include <iostream>
47 #include <string>
48 #include <deque>
49 
50 //From bpp-core:
51 #include <Bpp/Numeric/DataTable.h>
52 
53 namespace bpp {
54 
63 {
64  private:
65  std::string referenceSpecies_;
66  std::string targetSpecies_;
67  std::map<std::string, SequenceFeatureSet*> inputFeaturesPerChr_;
68  std::ostream& output_;
70 
71  public:
84  MafIterator* iterator,
85  const std::string& referenceSpecies,
86  const std::string& targetSpecies,
87  const SequenceFeatureSet& features,
88  std::ostream& output,
89  bool outputClosestCoordinate = true) :
90  AbstractFilterMafIterator(iterator),
91  referenceSpecies_(referenceSpecies),
92  targetSpecies_(targetSpecies),
94  output_(output),
95  outputClosestCoordinate_(outputClosestCoordinate)
96  {
97  //Sort features per chromosome for a faster access:
98  std::set<std::string> seqIds = features.getSequences();
99  for (std::set<std::string>::iterator it = seqIds.begin();
100  it != seqIds.end();
101  ++it) {
102  {
103  inputFeaturesPerChr_[*it] = features.getSubsetForSequence(*it);
104  }
105  }
106  output_ << "chr.ref\tstrand.ref\tbegin.ref\tend.ref\tchr.target\tstrand.target\tbegin.target\tend.target" << std::endl;
107  }
108 
110  //Clean sorted features.
111  for (std::map<std::string, SequenceFeatureSet*>::iterator it = inputFeaturesPerChr_.begin();
112  it != inputFeaturesPerChr_.end();
113  it++) {
114  delete it->second;
115  }
116  }
117 
118  private:
120 
121 };
122 
123 } // end of namespace bpp.
124 
125 #endif //_COORDINATETRANSLATORMAFITERATOR_H_
Helper class for developping filter for maf blocks.
Definition: MafIterator.h:151
Translate features coordinates from one species to another, based on the alignment.
CoordinateTranslatorMafIterator(MafIterator *iterator, const std::string &referenceSpecies, const std::string &targetSpecies, const SequenceFeatureSet &features, std::ostream &output, bool outputClosestCoordinate=true)
Build a new CoordinateTranslator iterator.
std::map< std::string, SequenceFeatureSet * > inputFeaturesPerChr_
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.
SequenceFeatureSet * getSubsetForSequence(const std::string &id) const
std::set< std::string > getSequences() const