X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.h;h=b924775cf5b30436c1783714a758281cf072c32f;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=c38a7c97111b4bd842fb7038a6faaf2acedc5d53;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/classifyotucommand.h b/classifyotucommand.h
index c38a7c9..b924775 100644
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -25,9 +25,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "classify.otu";		}
 	string getCommandCategory()		{ return "Phylotype Analysis";	}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Classify.otu"; }
-
+	string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Classify.otu"; }
+	string getDescription()		{ return "find the concensus taxonomy for each OTU"; }
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -44,10 +45,8 @@ private:
 	map<string, string> nameMap;
 	map<string, string> taxMap;
 
-	int readNamesFile();
-	int readTaxonomyFile();
-	void removeConfidences(string&);
 	int process(ListVector*);
+	string addUnclassifieds(string, int);
 	vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); 	// returns the name of the "representative" taxonomy of given bin