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 "globaldata.hpp"
  16
  17
  18 /*****************************************************************/
  19 class PCACommand : public Command {
  20
  21 public:
  22         PCACommand(string);
  23         PCACommand();
  24         ~PCACommand();
  25         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32 private:
  33         GlobalData* globaldata;
  34
  35         bool abort, metric;
  36         string outputDir, mode, inputFile, label, groups;
  37         vector<string> outputNames, Groups;
  38         set<string> labels;
  39         map<string, vector<string> > outputTypes;
  40         LinearAlgebra linearCalc;
  41
  42         //vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
  43         int process(vector<SharedRAbundFloatVector*>&);
  44         void output(string, vector<string>, vector<vector<double> >&, vector<double>);
  45
  46 };
  47
  48 /*****************************************************************/
  49
  50 #endif
  51
  52