#include "command.hpp"
#include "listvector.hpp"
+#include "sequence.hpp"
class CreateDatabaseCommand : public Command {
public:
vector<string> setParameters();
string getCommandName() { return "create.database"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Create.database"; }
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>&);
+ ListVector* getList();
};