class HeatMapSimCommand : public Command {
public:
+ HeatMapSimCommand(string);
HeatMapSimCommand();
~HeatMapSimCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
+ void help();
private:
GlobalData* globaldata;
vector<Calculator*> heatCalculators;
ValidCalculators* validCalculator;
HeatMapSim* heatmap;
+ OptionParser* parser;
+ map<string, string> parameters;
+ map<string, string>::iterator it;
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string format, groups, label, calc, phylipfile, columnfile, namefile, outputDir;
+ vector<string> Estimators, Groups, outputNames;
+ map<string, vector<string> > outputTypes;
+
+ int runCommandShared();
+ int runCommandDist();
+
};