X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.h;h=45e377c3cbe1ac1ad735cd9c4f47d4c4c37c30a5;hb=a9dbc22713bfc056a797361dd757b1a5c98e1c01;hp=60bfb29a900dbabedcb49a23523b4b704e98352e;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 60bfb29..45e377c 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 {
@@ -20,32 +21,35 @@ 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:
-
+    GroupMap* groupMap;
+    CountTable* ct;
 	ListVector* list;
 	InputData* input;
-	string listfile, namefile, taxfile, label, outputDir;
+	string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
 	bool abort, allLines, probs;
 	int cutoff;
 	set<string> labels; //holds labels to be used
 	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 findConsensusTaxonomy(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
 	
 												
 };