moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / cooccurrencecommand.h

diff --git a/cooccurrencecommand.h b/cooccurrencecommand.h
deleted file mode 100644 (file)
index 8f60e08..0000000
--- a/cooccurrencecommand.h
+++ /dev/null
@@ -1,53 +0,0 @@
-#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
-
-