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 "sharedrabundvector.h"
  15 #include "sharedrabundfloatvector.h"
  16 #include "inputdata.h"
  17
  18 class CorrAxesCommand : public Command {
  19 public:
  20         CorrAxesCommand(string);
  21         CorrAxesCommand();
  22         ~CorrAxesCommand();
  23         vector<string> getRequiredParameters();
  24         vector<string> getValidParameters();
  25         vector<string> getRequiredFiles();
  26         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  27         int execute();
  28         void help();
  29
  30 private:
  31         GlobalData* globaldata;
  32         string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
  33         bool abort, pickedGroups;
  34         int numaxes;
  35         set<string> names;
  36
  37         vector<string> outputNames, Groups;
  38         map<string, vector<string> > outputTypes;
  39         vector<SharedRAbundVector*> lookup;
  40         vector<SharedRAbundFloatVector*> lookupFloat;
  41
  42         int getShared();
  43         int getSharedFloat();
  44         int convertToRelabund();
  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
  50 };
  51
  52
  53 #endif
  54
  55