8 * Created by Sarah Westcott on 5/15/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
14 #include "globaldata.hpp"
16 class AlignCommand : public Command {
24 GlobalData* globaldata;
25 string candidateFileName, templateFileName, distanceFileName;
27 float match, misMatch, gapOpen, gapExtend;