X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.h;h=b924775cf5b30436c1783714a758281cf072c32f;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=f6bf78dfacb99509ada0d5a87d948f9ffe3aacb2;hpb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;p=mothur.git

diff --git a/classifyotucommand.h b/classifyotucommand.h
index f6bf78d..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 "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