bpp-seq-omics  2.4.1
OrderFilterMafIterator.cpp
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1 //
2 // File: OrderFilterMafIterator.cpp
3 // Authors: Julien Dutheil
4 // Created: Sat Jan 20 2018
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (2018)
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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33 data to be ensured and, more generally, to use and operate it in the
34 same conditions as regards security.
35 
36 The fact that you are presently reading this means that you have had
37 knowledge of the CeCILL license and that you accept its terms.
38 */
39 
40 #include "OrderFilterMafIterator.h"
41 
42 //From bpp-seq:
43 //#include <Bpp/Seq/SequenceWithAnnotationTools.h>
44 //#include <Bpp/Seq/Container/VectorSiteContainer.h>
45 //#include <Bpp/Seq/SiteTools.h>
46 //#include <Bpp/Seq/SequenceWalker.h>
47 
48 using namespace bpp;
49 
50 //From the STL:
51 #include <string>
52 #include <numeric>
53 #include <ctime>
54 
55 using namespace std;
56 
58 {
59  //Get the reference species for coordinates:
60  if (! block.hasSequenceForSpecies(refSpecies_))
61  return true; //We consider a block with no reference sequence as ordered
62  const MafSequence& refSeq = block.getSequenceForSpecies(refSpecies_);
63  string chr = refSeq.getChromosome();
64  if (chr != currentChr_) {
65  currentChr_ = chr;
66  previousBlockStart_ = 0;
67  previousBlockStop_ = 0;
68  } else {
69  //Check that block are ordered according to reference sequence:
70  if (refSeq.start() < previousBlockStop_) {
71  if (refSeq.stop() < previousBlockStart_) {
72  //non-overlapping
73  if (unsortedBlockThrowsException_)
74  throw Exception("OrderFilterMafIterator: blocks are not ordered according to reference sequence: " + refSeq.getDescription() + "<!>" + TextTools::toString(previousBlockStart_) + ".");
75  if (unsortedBlockDiscarded_) {
76  if (logstream_) {
77  (*logstream_ << "ORDER FILTER: block " << refSeq.getDescription() << " is not sorted according to previous block and was discarded. Previous block started at " << previousBlockStart_ << " and ended at " << previousBlockStop_ << ".").endLine();
78  }
79  return false;
80  }
81  } else {
82  //overlapping
83  if (overlappingBlockThrowsException_)
84  throw Exception("OrderFilterMafIterator: blocks are overlapping according to reference sequence: " + refSeq.getDescription() + "<!>" + TextTools::toString(previousBlockStop_) + ".");
85  if (overlappingBlockDiscarded_) {
86  if (logstream_) {
87  (*logstream_ << "ORDER FILTER: block " << refSeq.getDescription() << " is overlapping with previous block and was discarded. Previous block started at " << previousBlockStart_ << " and ended at " << previousBlockStop_ << ".").endLine();
88  }
89  return false;
90  }
91  }
92  }
93  previousBlockStart_ = refSeq.start();
94  previousBlockStop_ = refSeq.stop();
95  }
96  return true;
97 }
98 
A synteny block data structure, the basic unit of a MAF alignement file.
Definition: MafBlock.h:57
bool hasSequenceForSpecies(const std::string &species) const
Definition: MafBlock.h:129
const MafSequence & getSequenceForSpecies(const std::string &species) const
Definition: MafBlock.h:139
A sequence class which is used to store data from MAF files.
Definition: MafSequence.h:64
std::string getDescription() const
Definition: MafSequence.h:188
const std::string & getChromosome() const
Definition: MafSequence.h:164
size_t start() const
Definition: MafSequence.h:116
size_t stop() const
Definition: MafSequence.h:121
bool parseBlock_(const MafBlock &block)
std::string toString(T t)