public:
- ListSeqsCommand(string);
- ~ListSeqsCommand(){};
+ ListSeqsCommand(string);
+ ListSeqsCommand();
+ ~ListSeqsCommand(){}
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
- vector<string> names;
- string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile;
+ vector<string> names, outputNames;
+ map<string, vector<string> > outputTypes;
+ string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
bool abort;
- void readFasta();
- void readName();
- void readGroup();
- void readAlign();
- void readList();
+ int readFasta();
+ int readName();
+ int readGroup();
+ int readAlign();
+ int readList();
+ int readTax();
};