X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.h;h=c6d65037516c495f391ceb983273b1b9a20010e1;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=972f30e8e0e008111d14bc49670dc926a98d360f;hpb=d5c8caf2d08b7ac6de30e33b1d19cfd246d08f03;p=mothur.git

diff --git a/readotucommand.h b/readotucommand.h
index 972f30e..c6d6503 100644
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -9,30 +9,38 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "readmatrix.hpp"
 #include "inputdata.h"
-
-/* The read.otu command parameter options are listfile, sabundfile, rabundfile and orderfile.  
-The read.otu command should be in the following format: 
-read.otu(listfile=yourListFile, orderfile=yourOrderFile). The listfile, sabundfile or rabundfile are required, but only one may be used. */
-
-class GlobalData;
+#include "groupmap.h"
+#include "sharedcommand.h"
 
 class ReadOtuCommand : public Command {
 public:
+	ReadOtuCommand(string);
 	ReadOtuCommand();
-	~ReadOtuCommand();
-	int execute();
+	~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;
-	ReadMatrix* read;
 	InputData* input;
-	string filename;
+	Command* shared;
+	GroupMap* groupMap;
+	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
+
 };
 
-#endif
\ No newline at end of file
+#endif