*
*/
-#include <iostream>
-#include <fstream>
#include "command.hpp"
#include "readtree.h"
#include "treemap.h"
class ReadTreeCommand : public Command {
public:
- ReadTreeCommand();
+ ReadTreeCommand(string);
+ ReadTreeCommand() { abort = true; calledHelp = true; }
~ReadTreeCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
+ void help();
private:
GlobalData* globaldata;
ReadTree* read;
TreeMap* treeMap;
- string filename;
+ string filename, treefile, groupfile, namefile;
+ bool abort;
+ map<string, string> nameMap;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
+
+ int readNamesFile();
+ int numUniquesInName;
+
};