public:
GetLineageCommand(string);
+ GetLineageCommand();
~GetLineageCommand(){};
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
vector<string> outputNames;
string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
bool abort, dups;
+ map<string, vector<string> > outputTypes;
int readFasta();
int readName();