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