public:
CatchAllCommand(string);
- ~CatchAllCommand() {};
+ CatchAllCommand();
+ ~CatchAllCommand() {}
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map< string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
GlobalData* globaldata;
- ReadOTUFile* read;
- InputData* input;
- string outputDir, sabundfile, rabundfile, listfile, format;
+ string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path;
bool abort, allLines;
set<string> labels;
+ vector<string> outputNames;
+ map< string, vector<string> > outputTypes;
+ vector<string> groups;
- string process(SAbundVector*);
+ string process(SAbundVector*, string);
+ int createSummaryFile(string, string, ofstream&);
+ vector<string> parseSharedFile(string);
+ string combineSummmary(vector<string>&);
};
/****************************************************************************/