changing command name classify.shared to classifyrf.shared

[mothur.git] / pcacommand.h

diff --git a/pcacommand.h b/pcacommand.h
index eedfcf35c58d508cb37ebc41416ca0a3bfc7b1c8..482ecc3fecf678cca5853eb9c1160f005204a604 100644 (file)
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -12,8 +12,7 @@
 
 #include "command.hpp"
 #include "linearalgebra.h"
-#include "globaldata.hpp"
-
+#include "sharedrabundfloatvector.h"
 
 /*****************************************************************/
 class PCACommand : public Command {
@@ -21,27 +20,32 @@ class PCACommand : public Command {
 public:
        PCACommand(string);     
        PCACommand();
-       ~PCACommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~PCACommand() {}
        
-private:
-       GlobalData* globaldata;
+       vector<string> setParameters();
+       string getCommandName()                 { return "pca";                                 }
+       string getCommandCategory()             { return "Hypothesis Testing";  }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       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"; }
+       string getDescription()         { return "pca"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
+       
+private:
+
        bool abort, metric;
-       string outputDir, mode, inputFile, label, groups;
+       string outputDir, mode, inputFile, label, groups, sharedfile, relabundfile;
        vector<string> outputNames, Groups;
        set<string> labels;
-       map<string, vector<string> > outputTypes;
        LinearAlgebra linearCalc;
        
        //vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
        int process(vector<SharedRAbundFloatVector*>&);
-       void output(string, vector<string>, vector<vector<double> >&, vector<double>);
+       void output(string, string, vector<string>, vector<vector<double> >&, vector<double>);
        
 };