bpp-seq-omics  2.4.1
SequenceStatisticsMafIterator.h
Go to the documentation of this file.
1 //
2 // File: SequenceStatisticsMafIterator.h
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 
40 #ifndef _SEQUENCESTATISTICSMAFITERATOR_H_
41 #define _SEQUENCESTATISTICSMAFITERATOR_H_
42 
43 #include "MafIterator.h"
44 #include "MafStatistics.h"
45 
46 //From the STL:
47 #include <iostream>
48 #include <string>
49 #include <deque>
50 
51 namespace bpp {
52 
67 {
68  private:
69  std::vector<MafStatistics*> statistics_;
70  std::vector<const BppNumberI*> results_;
71  std::vector<std::string> names_;
72 
73  public:
78  SequenceStatisticsMafIterator(MafIterator* iterator, const std::vector<MafStatistics*> statistics);
79 
80  private:
83  statistics_(iterator.statistics_),
84  results_(iterator.results_),
85  names_(iterator.names_)
86  {}
87 
89  {
90  statistics_ = iterator.statistics_;
91  results_ = iterator.results_;
92  names_ = iterator.names_;
93  return *this;
94  }
95 
96  public:
97  const std::vector<const BppNumberI*>& getResults() const { return results_; }
98  const std::vector<std::string>& getResultsColumnNames() const { return names_; }
99 
100  private:
102 
103 };
104 
105 } // end of namespace bpp.
106 
107 #endif //_SEQUENCESTATISTICSMAFITERATOR_H_
Helper class for developping filter for maf blocks.
Definition: MafIterator.h:151
A synteny block data structure, the basic unit of a MAF alignement file.
Definition: MafBlock.h:57
Interface to loop over maf alignment blocks.
Definition: MafIterator.h:59
Compute a series of sequence statistics for each block.
SequenceStatisticsMafIterator(MafIterator *iterator, const std::vector< MafStatistics * > statistics)
std::vector< const BppNumberI * > results_
std::vector< MafStatistics * > statistics_
const std::vector< const BppNumberI * > & getResults() const
SequenceStatisticsMafIterator(const SequenceStatisticsMafIterator &iterator)
SequenceStatisticsMafIterator & operator=(const SequenceStatisticsMafIterator &iterator)
const std::vector< std::string > & getResultsColumnNames() const