X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterdoturcommand.h;h=0f8657c6236baf9554a136b464118d9104b6dc93;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=da2f4a7c000bb8b2ed0737c2b57dcc5d2569ccae;hpb=6cf9539162b0fb0b5c0b99673e999df3cd717c55;p=mothur.git

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index da2f4a7..0f8657c 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 +22,22 @@ 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 getOutputFileNameTag(string, string);
+	string getHelpString();		
+	string getCitation() { return "Schloss 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"; }
+	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 +49,6 @@ private:
 	
 	void printData(string label);
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 };
 
 #endif