vector<string> setParameters();
string getCommandName() { return "count.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
-
+ string getDescription() { return "counts the number of sequences represented by each unique sequence in a namesfile"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string namefile, groupfile, outputDir, groups;
- bool abort;
- vector<string> Groups;
+ bool abort, large;
+ vector<string> Groups, outputNames;
+
+ int processSmall(string);
+ int processLarge(string);
+ map<int, string> processNameFile(string);
+ map<int, string> getGroupNames(string, set<string>&);
+
};
#endif