added command descriptions

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index bf9ccc00d0e7151ea4dce787b42265f092416bbd..c6d65037516c495f391ceb983273b1b9a20010e1 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -10,27 +10,33 @@
  */
 
 #include "command.hpp"
-#include "readotu.h"
 #include "inputdata.h"
 #include "groupmap.h"
 #include "sharedcommand.h"
 
-class GlobalData;
-
 class ReadOtuCommand : public Command {
 public:
        ReadOtuCommand(string);
-       ~ReadOtuCommand();
-       int execute();
-       void help();
+       ReadOtuCommand();
+       ~ReadOtuCommand() {}
+       
+       vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
+       string getCommandName()                 { return "read.otu";    }
+       string getCommandCategory()             { return "Hidden";      }
+       string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like collect.shared."; }   
+       string getCitation() { return "http://www.mothur.org/wiki/Read.otu"; }
+       string getDescription()         { return "read.otu"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
        InputData* input;
        Command* shared;
        GroupMap* groupMap;
        string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
-       vector<string> Groups;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used