1 #ifndef ANOSIMCOMMAND_H
2 #define ANOSIMCOMMAND_H
8 * Created by westcott on 2/14/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
14 #include "command.hpp"
18 class AnosimCommand : public Command {
21 AnosimCommand(string);
24 vector<string> getRequiredParameters();
25 vector<string> getValidParameters();
26 vector<string> getRequiredFiles();
27 map<string, vector<string> > getOutputFiles() { return outputTypes; }
34 map<string, vector<string> > outputTypes;
35 string outputDir, inputDir, designFileName, phylipFileName;
37 vector<vector<double> > convertToRanks(vector<vector<double> >);
38 double calcR(vector<vector<double> >, map<string, vector<int> >);
39 map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
40 double runANOSIM(ofstream&, vector<vector<double> >, map<string, vector<int> >, double);
42 vector< vector<double> > distanceMatrix;
43 vector<string> outputNames;
45 double experimentwiseAlpha;
46 vector< vector<string> > namesOfGroupCombos;