added cooccurence command

[mothur.git] / cooccurrencecommand.h

diff --git a/cooccurrencecommand.h b/cooccurrencecommand.h
new file mode 100644 (file)
index 0000000..da7cde8
--- /dev/null
+++ b/cooccurrencecommand.h
@@ -0,0 +1,53 @@
+#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 "Cooccurrence"; }
+       
+       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
+
+