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
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
|
#ifndef ___GAP__
#define ___GAP__
#include "definitions.h"
#include <iostream>
using namespace std;
class gaps {
public:
explicit gaps() {};
~gaps() {
for(int i=0; i<_gaps.size();++i){
gap* gap2delete = _gaps[i];
delete gap2delete;
}
};
////////////////////////////////////////////////////////////////////////// inner class
class gap {
public:
explicit gap(int coord_5p, int coord_3p, int seqID, int coord_5Abs):
_coord_5p(coord_5p), _coord_3p(coord_3p), _seqID(seqID),_coord_5Abs(coord_5Abs) {};
~gap() {};
int getCoord5() const {return _coord_5p;};
int getCoord3()const {return _coord_3p;};
int getSeqID() const {return _seqID;};
int getCoord5Abs() const {return _coord_5Abs;};
int getLength() const {return _coord_3p-_coord_5p+1;};
private:
int _coord_5p;
int _coord_3p;
int _seqID;
int _coord_5Abs;
};
////////////////////////////////////////////////////////////////////////// end
gap* operator[](const int i) {return _gaps[i];} // get the ID of the gap. Return the gap itself.
int numOfGaps(){return _gaps.size();}
/********************************************************************************************
insertNewGap
// Sort the vector containing all indels by I =(i1,i2), K =(k1,k2), I<K iff i1<k1 or i1=k1 and i2<k2
*********************************************************************************************/
void insertNewGap(int coord_5p, int coord_3p, int seqID, int coord_5Abs)
{
gap* gap_p = new gap(coord_5p, coord_3p,seqID, coord_5Abs);
//_gaps.push_back(gap_p);
vector<gap*>::iterator iter;
int position = 0;
iter = _gaps.begin();
while( iter!=_gaps.end() &&
( (*iter)->getCoord5() < coord_5p ||
((*iter)->getCoord5() <= coord_5p && (*iter)->getCoord3() < coord_3p) ) )
{
iter++;
position++;
}
_gaps.insert(iter, gap_p);
};
//////////////////////////////////////////////////////////////////////////
void insertNewGap(gap* gap_p){
vector<gap*>::iterator iter;
int position = 0;
iter = _gaps.begin();
while( iter!=_gaps.end() &&
( (*iter)->getCoord5() < gap_p->getCoord5() ||
((*iter)->getCoord5() <= gap_p->getCoord5() && (*iter)->getCoord3() < gap_p->getCoord3()) ) )
{
iter++;
position++;
}
_gaps.insert(iter, gap_p);
};
void insertNewGapNotSorted(gap* gap_p){
_gaps.push_back(gap_p);
};
//////////////////////////////////////////////////////////////////////////
void printGaps(){
vector<gap*>::iterator iter;
iter = _gaps.begin();
while( iter!=_gaps.end())
{
cout<<"Gap "<<(*iter)->getCoord5()<<" "<<(*iter)->getCoord3()<<endl;
iter++;
}
};
private:
vector<gap*> _gaps;
};
#endif
|
