class GetOTURepCommand : public Command {
public:
- GetOTURepCommand();
+ GetOTURepCommand(string);
~GetOTURepCommand();
- int execute();
+ int execute();
+ void help();
private:
GlobalData* globaldata;
SparseMatrix* matrix;
ListVector* list;
- ListVector* listOfNames;
ReadOTUFile* read;
InputData* input;
FastaMap* fasta;
GroupMap* groupMap;
- string filename, fastafile, namesfile, groupfile;
+ string filename, fastafile, listfile, namesfile, groupfile, line, label;
ofstream out;
ifstream in, inNames;
bool groupError;
-
+ bool abort, allLines;
+ set<int> lines; //hold lines to be used
+ set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix
- map<int, string>::iterator it;
- map<int, string>::iterator it2;
- map<string, int>::iterator it3;
void readNamesFile();
int process(ListVector*);