X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.h;h=b5e32d897b2dd824d81b257fff12517a6a90bc6f;hb=2df35fdeea85f574630d75b11fb5b08c39aec31a;hp=972f30e8e0e008111d14bc49670dc926a98d360f;hpb=d5c8caf2d08b7ac6de30e33b1d19cfd246d08f03;p=mothur.git

diff --git a/readotucommand.h b/readotucommand.h
index 972f30e..b5e32d8 100644
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -9,30 +9,32 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #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. */
+#include "groupmap.h"
+#include "sharedcommand.h"
 
 class GlobalData;
 
 class ReadOtuCommand : public Command {
 public:
-	ReadOtuCommand();
+	ReadOtuCommand(string);
 	~ReadOtuCommand();
 	int execute();
+	void help();
 	
 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;
+	vector<string> Groups;
+
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+
 };
 
-#endif
\ No newline at end of file
+#endif