bpp-seq-omics  2.4.1
RemoveEmptySequencesMafIterator.cpp
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1 //
2 // File: RemoveEmptySequencesMafIterator.cpp
3 // Authors: Julien Dutheil
4 // Created: Tue Apr 26 2016
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (2014)
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
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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
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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
37 knowledge of the CeCILL license and that you accept its terms.
38 */
39 
41 
42 using namespace bpp;
43 using namespace std;
44 
46 {
47  currentBlock_ = iterator_->nextBlock();
48  if (currentBlock_) {
49  for (size_t i = currentBlock_->getNumberOfSequences(); i > 0; --i) {
50  const MafSequence& seq = currentBlock_->getSequence(i - 1);
51  bool isEmpty = true;
52  if (unresolvedAsGaps_) {
53  for (size_t j = 0; isEmpty && j < currentBlock_->getNumberOfSites(); ++j) {
54  if (!AlphabetTools::DNA_ALPHABET.isUnresolved(seq[j]) && !AlphabetTools::DNA_ALPHABET.isGap(seq[j])) isEmpty = false;
55  }
56  } else {
57  for (size_t j = 0; isEmpty && j < currentBlock_->getNumberOfSites(); ++j) {
58  if (!AlphabetTools::DNA_ALPHABET.isGap(seq[j])) isEmpty = false;
59  }
60  }
61  if (isEmpty) {
62  currentBlock_->getAlignment().removeSequence(i - 1);
63  }
64  }
65  }
66  return currentBlock_;
67 }
68 
static const DNA DNA_ALPHABET
A synteny block data structure, the basic unit of a MAF alignement file.
Definition: MafBlock.h:57
A sequence class which is used to store data from MAF files.
Definition: MafSequence.h:64
bool isEmpty(const std::string &s)