1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
|
/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _BubbleData
#define _BubbleData
#include <code/Mock/common_functions.h>
#include <vector>
#include <map>
#include <stdio.h>
#include <stdlib.h>
#include <set>
using namespace std;
/*
* put some members in this class or else g++ don't like it. it makes otherwise the program segfault!
* Contains information on bubbles so they can be detected
* \author Sébastien Boisvert
*/
class BubbleData{
public:
// arcs with good coverage
std::vector<std::vector<Kmer> > m_BUBBLE_visitedVertices;
// all vertices.
std::vector<std::set<Kmer> > m_visitedVertices;
bool m_doChoice_bubbles_Detected;
bool m_doChoice_bubbles_Initiated;
map<Kmer,int> m_coverages;
};
#endif
|
