private:
set<string> names;
vector<string> outputNames;
- string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, outputDir;
- bool abort;
+ string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
+ bool abort, dups;
- void readFasta();
- void readName();
- void readGroup();
- void readAlign();
- void readAccnos();
- void readList();
+ int readFasta();
+ int readName();
+ int readGroup();
+ int readAlign();
+ int readAccnos();
+ int readList();
+ int readTax();
};