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 "sharedrabundvector.h"
15 #include "sharedrabundfloatvector.h"
16 #include "inputdata.h"
18 class CorrAxesCommand : public Command {
20 CorrAxesCommand(string);
23 vector<string> getRequiredParameters();
24 vector<string> getValidParameters();
25 vector<string> getRequiredFiles();
26 map<string, vector<string> > getOutputFiles() { return outputTypes; }
31 GlobalData* globaldata;
32 string axesfile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, method;
33 bool abort, pickedGroups;
37 vector<string> outputNames, Groups;
38 map<string, vector<string> > outputTypes;
39 vector<SharedRAbundVector*> lookup;
40 vector<SharedRAbundFloatVector*> lookupFloat;
44 int convertToRelabund();
45 int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
46 map<string, vector<float> > readAxes();
47 int calcPearson(map<string, vector<float> >&, ofstream&);