X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clusterdoturcommand.h;h=ccfe03bb74c42d43921f8a8224c210bc7a3a7ab0;hp=da2f4a7c000bb8b2ed0737c2b57dcc5d2569ccae;hb=615301e57c25e241356a9c2380648d117709458d;hpb=6cf9539162b0fb0b5c0b99673e999df3cd717c55

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index da2f4a7..ccfe03b 100644
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "nameassignment.hpp"
-#include "globaldata.hpp"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
@@ -23,17 +22,23 @@ class ClusterDoturCommand : public Command {
 public:
 	ClusterDoturCommand(string);
 	ClusterDoturCommand();
-	~ClusterDoturCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	~ClusterDoturCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "cluster.classic";		}
+	string getCommandCategory()		{ return "Clustering";			}
+    
+	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.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster.classic\n";}
+	string getDescription()		{ return "cluster your sequences into OTUs using DOTUR’s method"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	bool abort, hard;
-	string method, fileroot, tag, outputDir, phylipfile, namefile;
+	bool abort, hard, sim;
+	string method, fileroot, tag, outputDir, phylipfile, namefile, countfile;
 	double cutoff;
 	int precision, length;
 	ofstream sabundFile, rabundFile, listFile;
@@ -45,7 +50,6 @@ private:
 	
 	void printData(string label);
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 };
 
 #endif