1 /**
2  * Author: Mark Larkin
3  *
4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
5  */
6 #ifndef MSA_H
7 #define MSA_H
8 
9 #include <iomanip>
10 #include "ProfileBase.h"
11 #include "../alignment/Alignment.h"
12 //#include "../calcAlignSteps/Tree.h"
13 #include "../tree/AlignmentSteps.h"
14 #include "ProfileAlignAlgorithm.h"
15 
16 namespace clustalw
17 {
18 //using tree::AlignmentSteps;
19 
20 class MSA
21 {
22     public:
23         /* Functions */
24         int multiSeqAlign(Alignment* alnPtr, DistMatrix* distMat,
25             vector<int>* seqWeight, AlignmentSteps* progSteps, int iStart);
26         int seqsAlignToProfile(Alignment* alnPtr, DistMatrix* distMat, vector<int>* seqWeight, int iStart,
27                               string phylipName);
28         int calcPairwiseForProfileAlign(Alignment* alnPtr, DistMatrix* distMat);
29         int doProfileAlign(Alignment* alnPtr, DistMatrix* distMat, vector<int>* prof1Weight,
30                            vector<int>* prof2Weight);
31 
32         /* Attributes */
33 
34     private:
35         /* Functions */
36 
37         /* Attributes */
38 };
39 
40 }
41 #endif
42