-
Notifications
You must be signed in to change notification settings - Fork 0
/
LocalAligner.h
145 lines (123 loc) · 3.21 KB
/
LocalAligner.h
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
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
/**
* @file LocalAligner.h
* @author Amirhosein Afshinfard <afshinfard(at)ce(.)sharif(.)edu>
* <afshinfard(at)gmail(.)com>
* Damoon Nashta-ali <damoun_dna(at)yahoo(.)com>
* Bioinformatics Research Lab - Sharif Uiversity of Technology
*
* @cite
*
* @copyright (c) 2017
*
* Amirhosein Afshinfard <afshinfard(at)ce (.)sharif(.)edu>
* <afshinfard(at)gmail(.)com>
* Damoon Nashta-ali <damoun_dna(at)yahoo(.)com>
* Seyed Abolfazl Motahari <motahari(at)sharif(.)edu>
*
**/
#ifndef LocalAligner_h
#define LocalAligner_h
#include <iostream>
#include <string>
#include <vector>
#include <sstream>
#include <algorithm>
class LocalAligner {
public:
std::string mAlignmentSeqA;
std::string mAlignmentSeqB;
LocalAligner(std::string, std::string, int, int, int, int, int);
void process();
void backtrack();
void Print();
~LocalAligner();
int mScore, totalMismatch = 0, totalGap = 0, totalGapr = 0, totalGapfa = 0; //totalMatch = 0
std::string cigar;
std::string realCigar;
void produceCigar();
int MATCH;
int MISMATCH;
int GAP;
int counter;
int shift;
int NegativeInf;
int k;
private:
std::string mSeqA;
std::string mSeqB;
int** mD;
int weight(size_t, size_t);
std::string reverseCigar();
};
#endif // LOCALALIGNER_H
//#ifndef LocalAligner_h
//#define LocalAligner_h
//#include <iostream>
//#include <string>
//#include <vector>
//#include <sstream>
//#include <algorithm>
//class LocalAligner {
//public:
// std::string mAlignmentSeqA;
// std::string mAlignmentSeqB;
// LocalAligner(std::string, std::string, int, int, int, int, int);
// void process();
// void backtrack();
// void Print();
// ~LocalAligner();
// int mScore, totalMismatch = 0, totalGap = 0; //totalMatch = 0
// std::string cigar;
// std::string realCigar;
// void produceCigar();
// int MATCH;
// int MISMATCH;
// int GAP;
// int counter;
// int shift;
// int NegativeInf;
// int k;
//private:
// std::string mSeqA;
// std::string mSeqB;
// int** mD;
// int weight(size_t, size_t);
// std::string reverseCigar();
//};
//#endif // LOCALALIGNER_H
//// V2 :
////#ifndef LocalAligner_h
////#define LocalAligner_h
////#include <iostream>
////#include <string>
////#include <vector>
////#include <sstream>
////#include <algorithm>
////class LocalAligner {
////public:
//// std::string mAlignmentSeqA;
//// std::string mAlignmentSeqB;
//// LocalAligner(std::string, std::string, int, int, int, int, int);
//// void process();
//// void backtrack();
//// void Print();
//// ~LocalAligner();
//// int mScore, totalMismatch = 0, totalGap = 0, totalGapr = 0, totalGapfa = 0; //totalMatch = 0
//// std::string cigar;
//// std::string realCigar;
//// void produceCigar();
//// int MATCH;
//// int MISMATCH;
//// int GAP;
//// int counter;
//// int shift;
//// int NegativeInf;
//// int k;
////private:
//// std::string mSeqA;
//// std::string mSeqB;
//// int** mD;
//// int weight(size_t, size_t);
//// std::string reverseCigar();
////};
////#endif // LOCALALIGNER_H