X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.h;h=2e76057f1219b8c44785a5be9b6962043bbb68af;hb=5c5c0428f6d548c28a8b903ac80efed4f92d59db;hp=b924775cf5b30436c1783714a758281cf072c32f;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/classifyotucommand.h b/classifyotucommand.h
index b924775..2e76057 100644
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -13,6 +13,7 @@
 #include "command.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
+#include "counttable.h"
 
 
 class ClassifyOtuCommand : public Command {
@@ -27,17 +28,18 @@ public:
 	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 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 77:3219.\nhttp://www.mothur.org/wiki/Classify.otu"; }
 	string getDescription()		{ return "find the concensus taxonomy for each OTU"; }
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 
 private:
-
+    GroupMap* groupMap;
+    CountTable* ct;
 	ListVector* list;
 	InputData* input;
-	string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
+	string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
 	bool abort, allLines, probs;
 	int cutoff;
 	set<string> labels; //holds labels to be used