*
*/
-#include <Carbon/Carbon.h>
-#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.
class ReadDistCommand : public Command {
public:
- ReadDistCommand();
+ ReadDistCommand(string);
+ ReadDistCommand() {}
~ReadDistCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
+ void help();
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;
+ map<string, vector<string> > outputTypes;
+
+ bool abort, sim;
+
};
-#endif
\ No newline at end of file
+#endif