pcacommand.h

   1 #ifndef PCACOMMAND_H
   2 #define PCACOMMAND_H
   3
   4 /*
   5  *  pcacommand.h
   6  *  mothur
   7  *
   8  *  Created by westcott on 1/7/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "linearalgebra.h"
  15 #include "sharedrabundfloatvector.h"
  16
  17 /*****************************************************************/
  18 class PCACommand : public Command {
  19
  20 public:
  21         PCACommand(string);
  22         PCACommand();
  23         ~PCACommand() {}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "pca";                                 }
  27         string getCommandCategory()             { return "Hypothesis Testing";  }
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Pca"; }
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34
  35 private:
  36
  37         bool abort, metric;
  38         string outputDir, mode, inputFile, label, groups, sharedfile, relabundfile;
  39         vector<string> outputNames, Groups;
  40         set<string> labels;
  41         LinearAlgebra linearCalc;
  42
  43         //vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
  44         int process(vector<SharedRAbundFloatVector*>&);
  45         void output(string, vector<string>, vector<vector<double> >&, vector<double>);
  46
  47 };
  48
  49 /*****************************************************************/
  50
  51 #endif
  52
  53