adds group parameter to chimera.uchime so you can check for chimeras with template...

[mothur.git] / sequenceparser.h

diff --git a/sequenceparser.h b/sequenceparser.h
index fa838f0c2adf185eb76472479f47fce786882fc0..23fcb9ecc983e1cf59ef1fde1f976da80773a152 100644 (file)
--- a/sequenceparser.h
+++ b/sequenceparser.h
@@ -42,12 +42,17 @@ class SequenceParser {
                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
 };