#include "listvector.hpp"
#include "readotu.h"
#include "fastamap.h"
+#include "groupmap.h"
class GlobalData;
class BinSeqCommand : public Command {
public:
- BinSeqCommand();
+ BinSeqCommand(string);
+ BinSeqCommand();
~BinSeqCommand();
- int execute();
+ 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;
FastaMap* fasta;
- string filename, fastafile, namesfile;
+ GroupMap* groupMap;
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string filename, fastafile, namesfile, groupfile, label, outputDir;
ofstream out;
ifstream in, inNames;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
void readNamesFile();
+ int process(ListVector*);
};
#endif