*
*/
-#include <iostream>
-#include <fstream>
#include "command.hpp"
#include "readmatrix.hpp"
+#include "fullmatrix.h"
+#include "groupmap.h"
/* The read.dist command is used to read a distance matrix file.
The read.dist command parameter options are phylipfile, columnfile, namefile, cutoff and precision.
If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed. */
class NameAssignment;
-class GlobalData;
-
class ReadDistCommand : public Command {
public:
- ReadDistCommand();
- ~ReadDistCommand();
- int execute();
+ ReadDistCommand(string);
+ ReadDistCommand() { abort = true; calledHelp = true; }
+ ~ReadDistCommand() {}
+
+ vector<string> setParameters() { return outputNames; } //dummy doesn't really do anything
+ string getCommandName() { return "read.dist"; }
+ string getCommandCategory() { return "Hidden"; }
+ string getHelpString() { return "This command is no longer available. You can provide your distance files directly to the downstream commands like cluster."; }
+ string getCitation() { return "http://www.mothur.org/wiki/Read.dist"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
double cutoff;
int precision;
ReadMatrix* read;
- string filename, format, method;
+ FullMatrix* matrix;
+ GroupMap* groupMap;
+ string distFileName, format, method;
+ string phylipfile, columnfile, namefile, groupfile, outputDir;
NameAssignment* nameMap;
+ vector<string> outputNames;
+
+ bool abort, sim;
+
};
#endif