class DeconvoluteCommand : public Command {
public:
- DeconvoluteCommand(string);
- ~DeconvoluteCommand() { delete fastamap; };
+ DeconvoluteCommand(string);
+ DeconvoluteCommand();
+ ~DeconvoluteCommand() {}
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
- FastaMap* fastamap;
- ifstream in;
- ofstream out, outFasta;
- string filename, outputFileName, outFastafile;
+ string inFastaName, oldNameMapFName, outputDir;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
bool abort;
};