X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.h;h=a0baf1849d92935fec3ca360a135805d3c41ddbc;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=c38a7c97111b4bd842fb7038a6faaf2acedc5d53;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/classifyotucommand.h b/classifyotucommand.h
index c38a7c9..a0baf18 100644
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -26,8 +26,8 @@ public:
 	string getCommandName()			{ return "classify.otu";		}
 	string getCommandCategory()		{ return "Phylotype Analysis";	}
 	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()); }	
@@ -46,8 +46,8 @@ private:
 
 	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