X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.h;h=b924775cf5b30436c1783714a758281cf072c32f;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=0ac0288e5bcf1d8879105295e41ad632fce1bdf1;hpb=fc9c3ccee1fba93d9df72c26baa22628268fe79f;p=mothur.git

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 0ac0288..b924775 100644
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -19,15 +19,25 @@ class ClassifyOtuCommand : public Command {
 
 public:
 	ClassifyOtuCommand(string);
-	~ClassifyOtuCommand();
-	int execute();
-	void help();
+	ClassifyOtuCommand();
+	~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:
 
 	ListVector* list;
 	InputData* input;
-	string listfile, namefile, taxfile, label, outputDir;
+	string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
 	bool abort, allLines, probs;
 	int cutoff;
 	set<string> labels; //holds labels to be used
@@ -35,11 +45,9 @@ private:
 	map<string, string> nameMap;
 	map<string, string> taxMap;
 
-	int readNamesFile();
-	int readTaxonomyFile();
-	void removeConfidences(string&);
 	int process(ListVector*);
-	string findConcensusTaxonomy(int, ListVector*, int&); 	// returns the name of the "representative" taxonomy of given bin
+	string addUnclassifieds(string, int);
+	vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); 	// returns the name of the "representative" taxonomy of given bin
 	
 												
 };