X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sequenceparser.h;h=98438f648b6f61d4c89192f7333aedfccfeced36;hp=fa838f0c2adf185eb76472479f47fce786882fc0;hb=615301e57c25e241356a9c2380648d117709458d;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063

diff --git a/sequenceparser.h b/sequenceparser.h
index fa838f0..98438f6 100644
--- 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
 };