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
|
/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* This ObjectiveScore class is used to provide an objective function to score
* an alignment.
* It is used with iteration to improve an alignment.
*/
#ifndef OBJECTIVESCORE_H
#define OBJECTIVESCORE_H
#include "../general/clustalw.h"
#include "../substitutionMatrix/globalmatrix.h"
namespace clustalw
{
class Alignment;
typedef struct
{
int first;
int second;
} Pair;
class ObjectiveScore
{
public:
ObjectiveScore();
long getScore(const Alignment* alnToScore);
private:
float scoreLetters(int seq1, int seq2);
float scoreGaps(int seq1, int seq2);
void calcNormalisedSeqWeights(const vector<int>* seqWeight,
vector<float>* normSeqWeight);
long score;
int matrix[NUMRES][NUMRES];
const Alignment* alignToScore;
long scale;
int weightScale;
int sagaGapEx, sagaGapOp;
int gapPos1, gapPos2;
static const int BOTHGAPS = 0;
static const int NOGAPS = -1;
static const int GAPINSEQB = 1;
static const int GAPINSEQA = 2;
};
}
#endif
|
