bpp-seq-omics  2.4.1
SequenceFilterMafIterator.cpp
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1 //
2 // File: SequenceFilterMafIterator.cpp
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
30 professionals having in-depth computer knowledge. Users are therefore
31 encouraged to load and test the software's suitability as regards their
32 requirements in conditions enabling the security of their systems and/or
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 
41 
42 using namespace bpp;
43 
44 //From the STL:
45 #include <string>
46 #include <numeric>
47 
48 using namespace std;
49 
51 {
52  currentBlock_ = iterator_->nextBlock();
53  while (currentBlock_) {
54  map<string, unsigned int> counts;
55  for (size_t i = currentBlock_->getNumberOfSequences(); i > 0; --i) {
56  string species = currentBlock_->getSequence(i-1).getSpecies();
57  if (!VectorTools::contains(species_, species)) {
58  if (logstream_) {
59  (*logstream_ << "SEQUENCE FILTER: remove sequence '" << species << "' from current block " << currentBlock_->getDescription() << ".").endLine();
60  }
61  if (!keep_) {
62  currentBlock_->getAlignment().removeSequence(i - 1);
63  }
64  } else {
65  counts[species]++;
66  }
67  }
68  bool test = currentBlock_->getNumberOfSequences() == 0;
69  //Avoid a memory leak:
70  if (test) {
71  if (logstream_) {
72  (*logstream_ << "SEQUENCE FILTER: block " << currentBlock_->getDescription() << " is now empty. Try to get the next one.").endLine();
73  }
74  delete currentBlock_;
75  } else {
76  test = strict_ && (counts.size() != species_.size());
77  if (test) {
78  if (logstream_) {
79  (*logstream_ << "SEQUENCE FILTER: block " << currentBlock_->getDescription() << " does not contain all species and will be ignored. Try to get the next one.").endLine();
80  }
81  delete currentBlock_;
82  } else {
83  if (rmDuplicates_) {
84  test = false;
85  map<string, unsigned int>::iterator it;
86  for (it = counts.begin(); it != counts.end() && !(test = it->second > 1); it++) {}
87  if (test) {
88  if (logstream_) {
89  (*logstream_ << "SEQUENCE FILTER: block " << currentBlock_->getDescription() << " has two sequences for species '" << it->first << "' and will be ignored. Try to get the next one.").endLine();
90  }
91  delete currentBlock_;
92  } else {
93  return currentBlock_;
94  }
95  } else {
96  return currentBlock_;
97  }
98  }
99  }
100 
101  //Look for the next block:
102  currentBlock_ = iterator_->nextBlock();
103  }
104 
105  return currentBlock_;
106 }
107 
A synteny block data structure, the basic unit of a MAF alignement file.
Definition: MafBlock.h:57
const MafSequence & getSequence(const std::string &name) const
Definition: MafBlock.h:121
const std::string & getSpecies() const
Definition: MafSequence.h:162
static bool contains(const std::vector< T > &vec, T el)