X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=hclustercommand.h;h=1b8e9b7607df66c0a36621f31ced21772f36a909;hp=4c8fa9c9aa7811d31dc52e3b050ac0c1d5305184;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=b5a791c81d432082bf38755a08b33863f255341d

diff --git a/hclustercommand.h b/hclustercommand.h
index 4c8fa9c..1b8e9b7 100644
--- a/hclustercommand.h
+++ b/hclustercommand.h
@@ -11,7 +11,6 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
@@ -19,7 +18,7 @@
 #include "readcluster.h"
 
 /******************************************************************/
-//This command is an implementation of the HCluster algorythmn described in 
+//This command is an implementation of the HCluster algorithmn described in 
 //ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences by
 //Yijun Sun1,2,*, Yunpeng Cai2, Li Liu1, Fahong Yu1, Michael L. Farrell3, William McKendree3 
 //and William Farmerie1 1 
@@ -32,13 +31,24 @@
 class HClusterCommand : public Command {
 	
 public:
-	HClusterCommand(string);	
-	~HClusterCommand();
-	int execute();	
-	void help();
+	HClusterCommand(string);
+	HClusterCommand();	
+	~HClusterCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "hcluster";	}
+	string getCommandCategory()		{ return "Clustering";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Sun Y, Cai Y, Liu L, Yu F, Farrell ML, Mckendree W, Farmerie W (2009). ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76. \nhttp://www.mothur.org/wiki/Hcluster"; }
+	string getDescription()		{ return "cluster your sequences into OTUs using a distance matrix"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
 	HCluster* cluster;
 	ListVector* list;
 	RAbundVector* rabund;
@@ -46,13 +56,14 @@ private:
 	ListVector oldList;
 	ReadCluster* read;
 	
-	bool abort, sorted, print_start;
-	string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing;
+	bool abort, sorted, print_start, hard;
+	string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing, outputDir;
 	double cutoff;
 	int precision, length;
 	ofstream sabundFile, rabundFile, listFile;
 	time_t start;
 	unsigned long loops;
+	vector<string> outputNames;
 	
 	void printData(string label);
 };