4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
6 #ifndef PROFILEWITHSUB_H
7 #define PROFILEWITHSUB_H
9 #include "../alignment/Alignment.h"
10 #include "ProfileBase.h"
15 class ProfileWithSub : public ProfileBase
19 ProfileWithSub(int prfLen, int firstS, int lastS);
21 void calcProfileWithSub(SeqArray* seqArray, vector<int>* gaps,
22 int matrix[NUMRES][NUMRES], vector<int>* seqWeight);