1 #ifndef CORRAXESCOMMAND_H
2 #define CORRAXESCOMMAND_H
8 * Created by westcott on 12/22/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "sharedrabundfloatvector.h"
15 #include "inputdata.h"
18 class CorrAxesCommand : public Command {
20 CorrAxesCommand(string);
24 vector<string> setParameters();
25 string getCommandName() { return "corr.axes"; }
26 string getCommandCategory() { return "Hypothesis Testing"; }
27 string getHelpString();
30 void help() { m->mothurOut(getHelpString()); }
33 string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
34 bool abort, pickedGroups;
38 vector<string> outputNames, Groups;
39 vector<SharedRAbundFloatVector*> lookupFloat;
40 vector<string> metadataLabels;
42 int getSharedFloat(InputData*);
44 int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
45 map<string, vector<float> > readAxes();
46 int calcPearson(map<string, vector<float> >&, ofstream&);
47 int calcSpearman(map<string, vector<float> >&, ofstream&);
48 int calcKendall(map<string, vector<float> >&, ofstream&);