--- /dev/null
+#ifndef COOCCURRENCECOMMAND_H
+#define COOCCURRENCECOMMAND_H
+
+/*
+ * COOCCURRENCE.h
+ * Mothur
+ *
+ * Created by westcott on 11/10/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "trialswap2.h"
+#include "inputdata.h"
+#include "sharedrabundvector.h"
+
+
+class CooccurrenceCommand : public Command {
+
+public:
+
+ CooccurrenceCommand(string);
+ CooccurrenceCommand();
+ ~CooccurrenceCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "Cooccurrence"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Cooccurrence"; }
+ string getDescription() { return "calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance."; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+
+private:
+ string metric, matrix, outputDir;
+ string label, sharedfile, groups;
+ bool abort, allLines;
+ set<string> labels;
+ vector<string> outputNames, Groups;
+ int runs;
+
+ int getCooccurrence(vector<SharedRAbundVector*>&, ofstream&);
+
+};
+
+#endif
+
+