1 #ifndef INDICATORCOMMAND_H
2 #define INDICATORCOMMAND_H
8 * Created by westcott on 11/12/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
16 #include "sharedrabundvector.h"
17 #include "sharedrabundfloatvector.h"
18 #include "inputdata.h"
20 class IndicatorCommand : public Command {
22 IndicatorCommand(string);
26 vector<string> setParameters();
27 string getCommandName() { return "indicator"; }
28 string getCommandCategory() { return "Hypothesis Testing"; }
29 string getHelpString();
32 void help() { m->mothurOut(getHelpString()); }
38 string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
40 vector<string> outputNames, Groups;
41 vector<SharedRAbundVector*> lookup;
42 vector<SharedRAbundFloatVector*> lookupFloat;
46 int GetIndicatorSpecies(Tree*&);
47 set<string> getDescendantList(Tree*&, int, map<int, set<string> >, map<int, set<int> >&);
48 vector<float> getValues(vector< vector<SharedRAbundVector*> >&);
49 vector<float> getValues(vector< vector<SharedRAbundFloatVector*> >&);
50 map<int, float> getDistToRoot(Tree*&);