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[mothur.git] / otuassociationcommand.h

diff --git a/otuassociationcommand.h b/otuassociationcommand.h
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+#ifndef OTUASSOCIATIONCOMMAND_H
+#define OTUASSOCIATIONCOMMAND_H
+
+/*
+ *  otuassociationcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 1/19/12.
+ *  Copyright 2012 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "sharedrabundfloatvector.h"
+#include "inputdata.h"
+
+
+class OTUAssociationCommand : public Command {
+public:
+       OTUAssociationCommand(string);
+       OTUAssociationCommand();
+       ~OTUAssociationCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "otu.association";                     }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Otu.association"; }
+       string getDescription()         { return "calculate the correlation coefficient for the otus in a shared/relabund file"; }
+       
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }  
+private:
+       
+       string sharedfile, relabundfile, groups, label, inputFileName, outputDir, method;
+       bool abort, pickedGroups, allLines;
+       set<string> labels;
+       
+       vector<string> outputNames, Groups;
+       int processShared();
+       int process(vector<SharedRAbundVector*>&);
+       int processRelabund();
+       int process(vector<SharedRAbundFloatVector*>&);
+       
+};
+
+
+#endif
+
+
+