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 "sharedrabundfloatvector.h"
17 /*****************************************************************/
18 class PCACommand : public Command {
25 vector<string> setParameters();
26 string getCommandName() { return "pca"; }
27 string getCommandCategory() { return "Hypothesis Testing"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Pca"; }
32 string getDescription() { return "pca"; }
35 void help() { m->mothurOut(getHelpString()); }
41 string outputDir, mode, inputFile, label, groups, sharedfile, relabundfile;
42 vector<string> outputNames, Groups;
44 LinearAlgebra linearCalc;
46 //vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
47 int process(vector<SharedRAbundFloatVector*>&);
48 void output(string, string, vector<string>, vector<vector<double> >&, vector<double>);
52 /*****************************************************************/