classifysharedcommand.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__classifysharedcommand__
  10 #define __Mothur__classifysharedcommand__
  11
  12 #include "command.hpp"
  13 #include "inputdata.h"
  14
  15 class ClassifySharedCommand : public Command {
  16 public:
  17   ClassifySharedCommand();
  18   ClassifySharedCommand(string);
  19   ~ClassifySharedCommand() {};
  20
  21   vector<string> setParameters();
  22   string getCommandName()                       { return "classify.shared";     }
  23    string getCommandCategory()          { return "OTU-Based Approaches";                }
  24
  25   string getHelpString();
  26     string getOutputPattern(string);
  27   string getCitation() { return "http://www.mothur.org/wiki/Classify.shared\n"; }
  28   string getDescription()               { return "description"; }
  29   int execute();
  30
  31   void help() { m->mothurOut(getHelpString()); }
  32
  33 private:
  34     bool abort;
  35     string outputDir;
  36     vector<string> outputNames, Groups;
  37
  38     string sharedfile, designfile, otupersplit, splitcriteria;
  39     set<string> labels;
  40     bool allLines;
  41
  42     int processors;
  43     bool useTiming;
  44
  45     GroupMap designMap;
  46
  47     int numDecisionTrees;
  48     string treeSplitCriterion, optimumFeatureSubsetSelectionCriteria;
  49     bool doPruning, discardHighErrorTrees;
  50     double pruneAggressiveness, highErrorTreeDiscardThreshold, featureStandardDeviationThreshold;
  51
  52     void processSharedAndDesignData(vector<SharedRAbundVector*> lookup);
  53 };
  54
  55 #endif /* defined(__Mothur__classifysharedcommand__) */