string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
+ string getDescription() { return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
set<string> names;
- string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+ map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
+ //then the other files need to change the unique name in their file to match.
+ //only add the names that need to be changed to keep the map search quick
+ string accnosfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
bool abort;
vector<string> outputNames, Groups;
GroupMap* groupMap;
int readList();
int readTax();
int fillNames();
+ int readShared();
+ int readDesign();
};