class SharedCommand : public Command {
public:
- SharedCommand();
+ SharedCommand(string);
+ SharedCommand();
~SharedCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help() {}
private:
void printSharedData(vector<SharedRAbundVector*>);
- void createMisMatchFile();
+ int createMisMatchFile();
+ int readOrderFile();
+ bool isValidGroup(string, vector<string>);
+ int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+ map<string, vector<string> > outputTypes;
+
GlobalData* globaldata;
ReadOTUFile* read;
SharedListVector* SharedList;
InputData* input;
GroupMap* groupMap;
+ vector<string> groups, outputNames, order;
ofstream out;
- string filename, fileroot;
- bool firsttime;
+ string filename, fileroot, outputDir;
+ bool firsttime, pickedGroups;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;