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 "globaldata.hpp"
  17 #include "sharedrabundvector.h"
  18 #include "sharedrabundfloatvector.h"
  19 #include "inputdata.h"
  20
  21 class IndicatorCommand : public Command {
  22 public:
  23         IndicatorCommand(string);
  24         IndicatorCommand();
  25         ~IndicatorCommand();
  26         vector<string> getRequiredParameters();
  27         vector<string> getValidParameters();
  28         vector<string> getRequiredFiles();
  29         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  30         int execute();
  31         void help();
  32
  33 private:
  34         GlobalData* globaldata;
  35         ReadTree* read;
  36         TreeMap* treeMap;
  37         string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir;
  38         bool abort;
  39         vector<string> outputNames, Groups;
  40         map<string, vector<string> > outputTypes;
  41         vector<SharedRAbundVector*> lookup;
  42         vector<SharedRAbundFloatVector*> lookupFloat;
  43
  44         int getShared();
  45         int getSharedFloat();
  46         int GetIndicatorSpecies(Tree*&);
  47         set<string> getDescendantList(Tree*&, int, map<int, set<string> >, map<int, set<int> >&);
  48         vector<float> getValues(vector< vector<SharedRAbundVector*> >&);
  49         vector<float> getValues(vector< vector<SharedRAbundFloatVector*> >&);
  50         map<int, float> getDistToRoot(Tree*&);
  51
  52 };
  53
  54
  55 #endif
  56