X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.h;h=c6d65037516c495f391ceb983273b1b9a20010e1;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=beb2f4bcbfe31ed89bdb2f9c393585a4ffae3667;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/readotucommand.h b/readotucommand.h
index beb2f4b..c6d6503 100644
--- 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;
-	vector<string> Groups;
+	string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
+	vector<string> Groups, outputNames;
+	map<string, vector<string> > outputTypes;
 
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used