*
*/
-#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