4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
6 #ifndef PROFILEALIGNALGORITHM_H
7 #define PROFILEALIGNALGORITHM_H
10 #include "../alignment/Alignment.h"
14 class ProfileAlignAlgorithm
17 virtual ~ProfileAlignAlgorithm(){};
20 virtual int profileAlign(Alignment* alnPtr, DistMatrix* distMat, vector<int>* group,
29 vector<int> alnWeight;