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

[mothur.git] / getsabundcommand.h

diff --git a/getsabundcommand.h b/getsabundcommand.h
index b5363e1bce548af4af74408593d855cac4da973c..d17574f57a8b33e3a0625ae056d604859736e036 100644 (file)
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -13,33 +13,28 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sabundvector.hpp"
 
-class GlobalData;
-
 class GetSAbundCommand : public Command {
 public:
        GetSAbundCommand(string);
        GetSAbundCommand();
-       ~GetSAbundCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~GetSAbundCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.sabund";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
-       string filename, format;
+       string filename, format, inputfile, listfile, rabundfile, outputDir;
        ofstream out;
-       ReadOTUFile* read;
-       OrderVector* order;
        InputData* input;
        SAbundVector* sabund;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used