vector<string> setParameters();
string getCommandName() { return "create.database"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+
string getHelpString();
+ string getOutputPattern(string);
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"; }
private:
bool abort;
- string listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
+ string sharedfile, listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir, countfile;
vector<string> outputNames;
vector<int> readFasta(vector<Sequence>&);
- vector<int> readTax(vector<string>&);
- int readNames(map<string, string>&);
+ vector<int> readTax(vector<string>&, vector<string>&);
ListVector* getList();
+ vector<SharedRAbundVector*> getShared();
+ int findIndex(vector<string>&, string);
};