X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.h;h=b924775cf5b30436c1783714a758281cf072c32f;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=e81c246201f36b7904d26b702748e1ba653dff66;hpb=a5af3313f0221a8b41aa362d72eadb60a4dd6e27;p=mothur.git

diff --git a/classifyotucommand.h b/classifyotucommand.h
index e81c246..b924775 100644
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -20,13 +20,18 @@ class ClassifyOtuCommand : public Command {
 public:
 	ClassifyOtuCommand(string);
 	ClassifyOtuCommand();
-	~ClassifyOtuCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~ClassifyOtuCommand() {}
+	
+	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()); }	
 
 private:
 
@@ -39,12 +44,9 @@ private:
 	vector<string> outputNames;
 	map<string, string> nameMap;
 	map<string, string> taxMap;
-	map<string, vector<string> > outputTypes;
 
-	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