bpp-seq-omics  2.4.1
SequenceStreamToMafIterator.cpp
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1 //
2 // File: MafAlignmentParser.h
3 // Authors: Julien Dutheil
4 // Created: Tue Apr 27 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,
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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 #include <Bpp/Text/TextTools.h>
43 
44 using namespace std;
45 using namespace bpp;
46 
47 MafBlock* SequenceStreamToMafIterator::analyseCurrentBlock_()
48 {
49  unique_ptr<MafBlock> block(new MafBlock());
50 
51  MafSequence mafSeq;
52  if (stream_->eof()) return 0;
53 
54  seqStream_->nextSequence(*stream_, mafSeq);
55  //Check if sequence name contains meta information:
56  string meta = mafSeq.getName();
57  StringTokenizer st(meta, ":");
58  if (st.numberOfRemainingTokens() == 5) {
59  string species = st.nextToken();
60  string chr = st.nextToken();
61  unsigned int start = TextTools::to<unsigned int>(st.nextToken());
62  if (!zeroBasedCoords_)
63  start--;
64  string strand = st.nextToken();
65  unsigned int length = TextTools::to<unsigned int>(st.nextToken());
66  mafSeq.setName(species + "." + chr);
67  mafSeq.setStrand(strand[0]);
68  mafSeq.setStart(start);
69  if (mafSeq.size() != length)
70  throw Exception("SequenceStreamToMafIterator::analyseCurrentBlock_. Sequence size does not match its header specification: expected " + TextTools::toString(length) + " and found " + TextTools::toString(mafSeq.size()));
71  }
72  block->addSequence(mafSeq);
73 
74  return block.release();
75 }
76 
virtual size_t size() const=0
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
void setName(const std::string &name)
Definition: MafSequence.h:142
void setStart(size_t begin)
Definition: MafSequence.h:172
void setStrand(char s)
Definition: MafSequence.h:184
const std::string & getName() const
size_t numberOfRemainingTokens() const
const std::string & nextToken()