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

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index eb0ca8f7832e5f1877a172fa0449a3ae29e5416f..d1dc5b7fc73726b09d9dce49a71015c0f70d70da 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -15,22 +15,21 @@
 #include "groupmap.h"
 #include "sharedcommand.h"
 
-class GlobalData;
-
 class ReadOtuCommand : public Command {
 public:
        ReadOtuCommand(string);
        ReadOtuCommand();
-       ~ReadOtuCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~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."; }   
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
        InputData* input;
        Command* shared;
        GroupMap* groupMap;