removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / getrabundcommand.h

diff --git a/getrabundcommand.h b/getrabundcommand.h
index e853ac5f913a1d758e7a633510478ad30449feec..dd0cefc89457cb114596c988c35b6be59c650547 100644 (file)
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -13,33 +13,31 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "listvector.hpp"
 
-class GlobalData;
 
 class GetRAbundCommand : public Command {
 public:
        GetRAbundCommand(string);
        GetRAbundCommand();
-       ~GetRAbundCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~GetRAbundCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.rabund";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       string filename;
+       
+       string filename, listfile, sabundfile, inputfile, format, outputDir;
        ofstream out;
-       ReadOTUFile* read;
        InputData* input;
-       ListVector* list;
        RAbundVector* rabund;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 
        bool abort, allLines, sorted;
        set<string> labels; //holds labels to be used