changing command name classify.shared to classifyrf.shared

[mothur.git] / sequenceparser.h

diff --git a/sequenceparser.h b/sequenceparser.h
index fa838f0c2adf185eb76472479f47fce786882fc0..98438f648b6f61d4c89192f7333aedfccfeced36 100644 (file)
--- a/sequenceparser.h
+++ b/sequenceparser.h
@@ -36,18 +36,22 @@ class SequenceParser {
                int getNumGroups();
                vector<string> getNamesOfGroups();      
                bool isValidGroup(string);  //return true if string is a valid group
-               string getGroup(string);        //returns group of a specific sequence
                
                int getNumSeqs(string);         //returns the number of unique sequences in a specific group
                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
 };