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
|
/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifndef MSA_H
#define MSA_H
#include <iomanip>
#include "ProfileBase.h"
#include "../alignment/Alignment.h"
//#include "../calcAlignSteps/Tree.h"
#include "../tree/AlignmentSteps.h"
#include "ProfileAlignAlgorithm.h"
namespace clustalw
{
//using tree::AlignmentSteps;
class MSA
{
public:
/* Functions */
int multiSeqAlign(Alignment* alnPtr, DistMatrix* distMat,
vector<int>* seqWeight, AlignmentSteps* progSteps, int iStart);
int seqsAlignToProfile(Alignment* alnPtr, DistMatrix* distMat, vector<int>* seqWeight, int iStart,
string phylipName);
int calcPairwiseForProfileAlign(Alignment* alnPtr, DistMatrix* distMat);
int doProfileAlign(Alignment* alnPtr, DistMatrix* distMat, vector<int>* prof1Weight,
vector<int>* prof2Weight);
/* Attributes */
private:
/* Functions */
/* Attributes */
};
}
#endif
|
