X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.h;h=a0baf1849d92935fec3ca360a135805d3c41ddbc;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=7f15c71c1847421abb88c3202d96e8ca7015837a;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 7f15c71..a0baf18 100644
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -26,6 +26,8 @@ public:
 	string getCommandName()			{ return "classify.otu";		}
 	string getCommandCategory()		{ return "Phylotype Analysis";	}
 	string getHelpString();	
+	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()); }	
@@ -44,8 +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