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         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
  32
  33         GlobalData* globaldata;
  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         map<string, vector<string> > outputTypes;
  41         vector<SharedRAbundFloatVector*> lookupFloat;
  42         vector<string> metadataLabels;
  43
  44         int getSharedFloat(InputData*);
  45         int getMetadata();
  46         int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
  47         map<string, vector<float> > readAxes();
  48         int calcPearson(map<string, vector<float> >&, ofstream&);
  49         int calcSpearman(map<string, vector<float> >&, ofstream&);
  50         int calcKendall(map<string, vector<float> >&, ofstream&);
  51
  52 };
  53
  54
  55 #endif
  56
  57