indicatorcommand.h

   1 #ifndef INDICATORCOMMAND_H
   2 #define INDICATORCOMMAND_H
   3
   4 /*
   5  *  indicatorcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 11/12/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "readtree.h"
  15 #include "treemap.h"
  16 #include "sharedrabundvector.h"
  17 #include "sharedrabundfloatvector.h"
  18 #include "inputdata.h"
  19
  20 class IndicatorCommand : public Command {
  21 public:
  22         IndicatorCommand(string);
  23         IndicatorCommand();
  24         ~IndicatorCommand(){}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "indicator";                           }
  28         string getCommandCategory()             { return "Hypothesis Testing";          }
  29         string getHelpString();
  30         string getCitation() { return "http://www.mothur.org/wiki/Indicator"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35 private:
  36         ReadTree* read;
  37         TreeMap* treeMap;
  38         GroupMap* designMap;
  39         string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
  40         bool abort;
  41         vector<string> outputNames, Groups;
  42         vector<SharedRAbundVector*> lookup;
  43         vector<SharedRAbundFloatVector*> lookupFloat;
  44
  45         int getShared();
  46         int getSharedFloat();
  47         int GetIndicatorSpecies(Tree*&);
  48         set<string> getDescendantList(Tree*&, int, map<int, set<string> >, map<int, set<int> >&);
  49         vector<float> getValues(vector< vector<SharedRAbundVector*> >&);
  50         vector<float> getValues(vector< vector<SharedRAbundFloatVector*> >&);
  51         map<int, float> getDistToRoot(Tree*&);
  52
  53 };
  54
  55
  56 #endif
  57