bpp-seq  2.2.0
SequenceWithAnnotationTools.cpp
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1 //
2 // File: SequenceWithAnnotationTools.cpp
3 // Authors: Julien Dutheil
4 // Created on: 06 Sep 2010
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (Sep 06, 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
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31 encouraged to load and test the software's suitability as regards their
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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 
42 
43 using namespace bpp;
44 using namespace std;
45 
46 const string SequenceMask::MASK = "Boolean mask";
47 
48 /******************************************************************************/
49 
51 {
52  mask_.clear();
53  mask_.insert(mask_.begin(), event.getSymbolList()->size(), false);
54 }
55 
56 /******************************************************************************/
57 
59 {
60  mask_.insert(mask_.begin() + static_cast<ptrdiff_t>(event.getPosition()),
61  event.getLength(), false);
62 }
63 
64 /******************************************************************************/
65 
67 {
68  mask_.erase(mask_.begin() + static_cast<ptrdiff_t>(event.getPosition()),
69  mask_.begin() + static_cast<ptrdiff_t>(event.getPosition() + event.getLength()));
70 }
71 
72 /******************************************************************************/
73 
75 {
76  const CaseMaskedAlphabet* cma = dynamic_cast<const CaseMaskedAlphabet*>(seq.getAlphabet());
77  if (cma) {
78  SequenceWithAnnotation* seqa = new SequenceWithAnnotation(seq.getName(), seq.toString(), seq.getComments(), seq.getAlphabet());
79  vector<bool> mask(seq.size());
80  for (unsigned int i = 0; i < seq.size(); ++i) {
81  mask[i] = cma->isMasked(seq[i]);
82  }
83  seqa->addAnnotation(new SequenceMask(mask));
84  return seqa;
85  } else {
86  throw AlphabetException("SequenceWithAnnotationTools::createMaskAnnotation. Alphabet should be a CaseMaskedAlphabet.", seq.getAlphabet());
87  }
88 }
89 
90 /******************************************************************************/
91 
virtual size_t getLength() const
Definition: SymbolList.h:427
This alphabet is used to deal NumericAlphabet.
STL namespace.
bool isMasked(int state) const
virtual void addAnnotation(SequenceAnnotation *anno)
Add a new annotation to the sequence.
SequenceWithAnnotation * createMaskAnnotation(const Sequence &seq)
Parse a sequence with a CaseMaskedAlphabet and creates a new SequenceWithAnnotation object with origi...
void afterSequenceInserted(const SymbolListInsertionEvent &event)
void afterSequenceDeleted(const SymbolListDeletionEvent &event)
The alphabet exception base class.
An implementation of the Sequence interface that supports annotation.
void afterSequenceChanged(const SymbolListEditionEvent &event)
The sequence interface.
Definition: Sequence.h:74
static const std::string MASK
Case-sensitive letter alphabet.