corraxescommand.h

   1 #ifndef CORRAXESCOMMAND_H
   2 #define CORRAXESCOMMAND_H
   3
   4 /*
   5  *  corraxescommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 12/22/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "sharedrabundfloatvector.h"
  15 #include "inputdata.h"
  16
  17
  18 class CorrAxesCommand : public Command {
  19 public:
  20         CorrAxesCommand(string);
  21         CorrAxesCommand();
  22         ~CorrAxesCommand(){}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "corr.axes";                           }
  26         string getCommandCategory()             { return "Hypothesis Testing";          }
  27         string getHelpString();
  28         string getCitation() { return "http://www.mothur.org/wiki/Corr.axes"; }
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32 private:
  33
  34         string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
  35         bool abort, pickedGroups;
  36         int numaxes;
  37         set<string> names;
  38
  39         vector<string> outputNames, Groups;
  40         vector<SharedRAbundFloatVector*> lookupFloat;
  41         vector<string> metadataLabels;
  42
  43         int getSharedFloat(InputData*);
  44         int getMetadata();
  45         int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
  46         map<string, vector<float> > readAxes();
  47         int calcPearson(map<string, vector<float> >&, ofstream&);
  48         int calcSpearman(map<string, vector<float> >&, ofstream&);
  49         int calcKendall(map<string, vector<float> >&, ofstream&);
  50
  51 };
  52
  53
  54 #endif
  55
  56