public:
BinSeqCommand(string);
+ BinSeqCommand();
~BinSeqCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
InputData* input;
FastaMap* fasta;
GroupMap* groupMap;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
bool abort, allLines;
- set<int> lines; //hold lines to be used
set<string> labels; //holds labels to be used
- string filename, fastafile, namesfile, groupfile, line, label;
+ 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*, int);
+ int process(ListVector*);
};
#endif