*/
#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."; }
+
+ 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;
- 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