--- /dev/null
+#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
+
+
+