class ReadDistCommand : public Command {
public:
ReadDistCommand(string);
+ ReadDistCommand() {}
~ReadDistCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
ReadMatrix* read;
FullMatrix* matrix;
GroupMap* groupMap;
- string filename, format, method;
- string phylipfile, columnfile, namefile, groupfile;
+ string distFileName, format, method;
+ string phylipfile, columnfile, namefile, groupfile, outputDir;
NameAssignment* nameMap;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
- bool abort;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
+
+ bool abort, sim;
};