1 #ifndef OTUASSOCIATIONCOMMAND_H
2 #define OTUASSOCIATIONCOMMAND_H
5 * otuassociationcommand.h
8 * Created by westcott on 1/19/12.
9 * Copyright 2012 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "sharedrabundfloatvector.h"
16 #include "inputdata.h"
19 class OTUAssociationCommand : public Command {
21 OTUAssociationCommand(string);
22 OTUAssociationCommand();
23 ~OTUAssociationCommand(){}
25 vector<string> setParameters();
26 string getCommandName() { return "otu.association"; }
27 string getCommandCategory() { return "Hypothesis Testing"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://www.mothur.org/wiki/Otu.association"; }
32 string getDescription() { return "calculate the correlation coefficient for the otus in a shared/relabund file"; }
35 void help() { m->mothurOut(getHelpString()); }
38 string sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
39 bool abort, pickedGroups, allLines;
42 vector<SharedRAbundFloatVector*> metadataLookup;
43 vector< vector< double> > metadata;
45 vector<string> outputNames, Groups, metadataLabels;
47 int process(vector<SharedRAbundVector*>&);
48 int processRelabund();
49 int process(vector<SharedRAbundFloatVector*>&);