classifyrfsharedcommand.h

   1 //
   2 //  classifysharedcommand.h
   3 //  Mothur
   4 //
   5 //  Created by Abu Zaher Md. Faridee on 8/13/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #ifndef __Mothur__classifyrfsharedcommand__
  10 #define __Mothur__classifyrfsharedcommand__
  11
  12 #include "command.hpp"
  13 #include "inputdata.h"
  14
  15 class ClassifyRFSharedCommand : public Command {
  16 public:
  17   ClassifyRFSharedCommand();
  18   ClassifyRFSharedCommand(string);
  19   ~ClassifyRFSharedCommand() {};
  20
  21   vector<string> setParameters();
  22   string getCommandName()                       { return "classifyrf.shared";     }
  23   string getCommandCategory()           { return "OTU-Based Approaches";                }
  24   string getHelpString();
  25   string getOutputPattern(string);
  26   string getCitation() { return "http://www.mothur.org/wiki/Classifyrf.shared\n"; }
  27   string getDescription()               { return "implements the random forest machine learning algorithm to identify OTUs that can be used to differentiate between various groups of samples"; }
  28   int execute();
  29
  30   void help() { m->mothurOut(getHelpString()); }
  31
  32 private:
  33     bool abort;
  34     string outputDir;
  35     vector<string> outputNames, Groups;
  36
  37     string sharedfile, designfile;
  38     set<string> labels;
  39     bool allLines;
  40
  41     int processors;
  42     bool useTiming;
  43
  44     GroupMap designMap;
  45
  46     int numDecisionTrees;
  47     string treeSplitCriterion, optimumFeatureSubsetSelectionCriteria;
  48     bool doPruning, discardHighErrorTrees;
  49     double pruneAggressiveness, highErrorTreeDiscardThreshold, featureStandardDeviationThreshold;
  50
  51     void processSharedAndDesignData(vector<SharedRAbundVector*> lookup);
  52 };
  53
  54 #endif /* defined(__Mothur__classifyrfsharedcommand__) */