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