#include "command.hpp"
#include "listvector.hpp"
+#include "sequence.hpp"
class CreateDatabaseCommand : public Command {
public:
string getDescription() { return "creates database file that includes, abundances across groups, representative sequences, and taxonomy for each OTU"; }
- int execute() {};
+ int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
- string listfile, groupfile, repfastafile, repnamesfile, constaxonomyfile, label, outputDir;
+ string listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
vector<string> outputNames;
- int readFasta();
- int readNames();
- int readTax();
- int processList(ListVector*&);
+ vector<int> readFasta(vector<Sequence>&);
+ vector<int> readTax(vector<string>&);
+ int readNames(map<string, string>&);
+ ListVector* getList();
};