*
*/
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
#include "command.hpp"
#include "readmatrix.hpp"
#include "inputdata.h"
+#include "groupmap.h"
+#include "sharedcommand.h"
+#include "parselistcommand.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. */
+/* The read.otu must be run before you execute a collect.single, rarefaction.single, summary.single,
+collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund
+upon completion of the cluster command or you may use your own. The read.otu command parameter options are
+listfile, rabundfile, sabundfile, groupfile and orderfile. The reaad.otu command can be used in two ways.
+The first is to read a listfile, rabundfile or sabundfile and run the collect.single, rarefaction.single or summary.single.
+For this use the read.otu command should be in the following format: read.otu(listfile=yourListFile, orderfile=yourOrderFile).
+The listfile, rabundfile or sabundfile parameter is required, but you may only use one of them.
+The second way to use the read.otu command is to read a listfile and a groupfile so you can use the collect.shared,
+rarefaction.shared or summary.shared commands. In this case the read.otu command should be in the following format:
+read.otu(listfile=yourListFile, groupfile=yourGroupFile). The listfile parameter and groupfile paramaters are required.
+When using the command the second way read.otu command parses the .list file and separates it into groups.
+It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. */
class GlobalData;
GlobalData* globaldata;
ReadMatrix* read;
InputData* input;
+ Command* shared;
+ Command* parselist;
+ GroupMap* groupMap;
string filename;
};
-#endif
\ No newline at end of file
+#endif