vector<Sequence> getSeqs(string); //returns unique sequences in a specific group
map<string, string> getNameMap(string); //returns seqName -> namesOfRedundantSeqs separated by commas for a specific group - the name file format, but each line is parsed by group.
+ int getSeqs(string, string, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false
+ int getNameMap(string, string); //print seqName -> namesOfRedundantSeqs separated by commas for a specific group - group, filename
+
+ map<string, string> getAllSeqsMap(){ return allSeqsMap; } //returns map where the key=sequenceName and the value=representativeSequence - helps us remove duplicates after group by group processing
private:
GroupMap* groupMap;
MothurOut* m;
int numSeqs;
+ map<string, string> allSeqsMap;
map<string, vector<Sequence> > seqs; //a vector for each group
map<string, map<string, string> > nameMapPerGroup; //nameMap for each group
};