X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=hclustercommand.h;h=d1074070420fc89347a65b8fa8c0448c953c8881;hp=7351cef71a6edad1a3b1484cbe437d9dd6899e39;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=72ebb6fa35b45b149812d47c2b1cb8acaca64659

diff --git a/hclustercommand.h b/hclustercommand.h
index 7351cef..d107407 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"
@@ -28,27 +27,28 @@
 //University of Florida, Gainesville, FL 32610-3622 and 3Materials Technology Directorate, Air Force Technical 
 //Applications Center, 1030 S. Highway A1A, Patrick AFB, FL 32925-3002, USA 
 //Received January 28, 2009; Revised April 14, 2009; Accepted April 15, 2009 
-
-/******************************************************************/
-
-
-/************************************************************/
-struct seqDist {
-	int seq1;
-	int seq2;
-	float dist;
-};
 /************************************************************/
 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;
@@ -56,23 +56,16 @@ private:
 	ListVector oldList;
 	ReadCluster* read;
 	
-	bool abort;
-
-	string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort;
+	bool abort, sorted, print_start, hard;
+	string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing, outputDir;
 	double cutoff;
-	string showabund, timing;
 	int precision, length;
 	ofstream sabundFile, rabundFile, listFile;
-	//ifstream in;
-	seqDist next;
-	bool exitedBreak, sorted;
-
-	bool print_start;
 	time_t start;
 	unsigned long loops;
+	vector<string> outputNames;
 	
 	void printData(string label);
-	vector<seqDist> getSeqs(ifstream&);
 };
 
 /************************************************************/