8 * Created by westcott on 1/7/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "linearalgebra.h"
15 #include "globaldata.hpp"
18 /*****************************************************************/
19 class PCACommand : public Command {
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
33 GlobalData* globaldata;
36 string outputDir, mode, inputFile, label, groups;
37 vector<string> outputNames, Groups;
39 map<string, vector<string> > outputTypes;
40 LinearAlgebra linearCalc;
42 vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
43 int process(vector<SharedRAbundFloatVector*>&);
44 void output(string, vector<string>, vector<vector<double> >&, vector<double>);
48 /*****************************************************************/