changes while testing

[mothur.git] / classifysharedcommand.h

diff --git a/classifysharedcommand.h b/classifysharedcommand.h
deleted file mode 100755 (executable)
index 7a6907f..0000000
--- a/classifysharedcommand.h
+++ /dev/null
@@ -1,54 +0,0 @@
-//
-//  classifysharedcommand.h
-//  Mothur
-//
-//  Created by Abu Zaher Md. Faridee on 8/13/12.
-//  Copyright (c) 2012 Schloss Lab. All rights reserved.
-//
-
-#ifndef __Mothur__classifysharedcommand__
-#define __Mothur__classifysharedcommand__
-
-#include "command.hpp"
-#include "inputdata.h"
-
-class ClassifySharedCommand : public Command {
-public:
-  ClassifySharedCommand();
-  ClassifySharedCommand(string);
-  ~ClassifySharedCommand() {};
-  
-  vector<string> setParameters();
-  string getCommandName()                      { return "classify.shared";     }
-  string getCommandCategory()          { return "OTU-Based Approaches";                }  
-  string getHelpString();      
-  string getOutputPattern(string);
-  string getCitation() { return "http://www.mothur.org/wiki/Classify.shared\n"; }
-  string getDescription()              { return "implements the random forest machine learning algorithm to identify OTUs that can be used to differentiate between various groups of samples"; }
-  int execute();
-  
-  void help() { m->mothurOut(getHelpString()); }
-
-private:
-    bool abort;
-    string outputDir;
-    vector<string> outputNames, Groups;
-  
-    string sharedfile, designfile;
-    set<string> labels;
-    bool allLines;
-  
-    int processors;
-    bool useTiming;
-
-    GroupMap designMap;
-  
-    int numDecisionTrees;
-    string treeSplitCriterion, optimumFeatureSubsetSelectionCriteria;
-    bool doPruning, discardHighErrorTrees;
-    double pruneAggressiveness, highErrorTreeDiscardThreshold, featureStandardDeviationThreshold;
-    
-    void processSharedAndDesignData(vector<SharedRAbundVector*> lookup);
-};
-
-#endif /* defined(__Mothur__classifysharedcommand__) */