4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
10 #include "ProfileBase.h"
11 #include "../alignment/Alignment.h"
12 //#include "../calcAlignSteps/Tree.h"
13 #include "../tree/AlignmentSteps.h"
14 #include "ProfileAlignAlgorithm.h"
18 //using tree::AlignmentSteps;
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,
28 int calcPairwiseForProfileAlign(Alignment* alnPtr, DistMatrix* distMat);
29 int doProfileAlign(Alignment* alnPtr, DistMatrix* distMat, vector<int>* prof1Weight,
30 vector<int>* prof2Weight);