X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classifyotucommand.h;h=c0a822070fa9a8b0b570f05e1ede727e19ead48b;hp=1077781e59b998892d699bf09b34c897a0a15375;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=8130ff9b30d872c578963f8d6f24af821b1ec33c

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 1077781..c0a8220 100644
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -13,33 +13,44 @@
 #include "command.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
+#include "counttable.h"
 
 
 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 getHelpString();	
+    string getOutputPattern(string);	
+	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;
-	bool abort, allLines, probs;
+	string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
+	bool abort, allLines, probs, persample;
 	int cutoff;
 	set<string> labels; //holds labels to be used
-	vector<string> outputNames;
+	vector<string> outputNames, groups;
 	map<string, string> nameMap;
 	map<string, string> taxMap;
 
-	int readNamesFile();
-	int readTaxonomyFile();
-	void removeConfidences(string&);
 	int process(ListVector*);
-	string findConsensusTaxonomy(int, ListVector*, int&); 	// returns the name of the "representative" taxonomy of given bin
+	string addUnclassifieds(string, int);
+	vector<string> findConsensusTaxonomy(vector<string>, int&, string&); 	// returns the name of the "representative" taxonomy of given bin
 	
 												
 };