X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clustercommand.h;h=cd9f47b07d9e8af9a6f04c014fabcfaf36a2818e;hp=5c57b69d1bd5dc0495925cb452df908ff5cb5b81;hb=615301e57c25e241356a9c2380648d117709458d;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0

diff --git a/clustercommand.h b/clustercommand.h
index 5c57b69..cd9f47b 100644
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -10,19 +10,18 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
 #include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
+#include "counttable.h"
 
 /* The cluster() command:
-	The cluster command can only be executed after a successful read.phylip or read.column command.   
 	The cluster command outputs a .list , .rabund and .sabund files.  
 	The cluster command parameter options are method, cuttoff and precision. No parameters are required.  
 	The cluster command should be in the following format: cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision).  
-	The acceptable methods are furthest, nearest and average.  If you do not provide a method the default algorythm is furthest neighbor.  
+	The acceptable methods are furthest, nearest and average.  If you do not provide a method the default algorithm is furthest neighbor.  
 	The cluster() command outputs three files *.list, *.rabund, and *.sabund.   */
 
 
@@ -30,23 +29,34 @@ class ClusterCommand : public Command {
 	
 public:
 	ClusterCommand(string);
+	ClusterCommand();
 	~ClusterCommand();
-	int execute();	
-	void help();
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "cluster";		}
+	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"; }
+	string getDescription()		{ return "cluster your sequences into OTUs using a distance matrix"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
 	Cluster* cluster;
-	SparseMatrix* matrix;
+	SparseDistanceMatrix* matrix;
 	ListVector* list;
 	RAbundVector* rabund;
 	RAbundVector oldRAbund;
 	ListVector oldList;
 
-	bool abort;
+	bool abort, hard, sim;
 
-	string method, fileroot, tag, outputDir;
+	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
 	double cutoff;
+    float adjust;
 	string showabund, timing;
 	int precision, length;
 	ofstream sabundFile, rabundFile, listFile;
@@ -57,6 +67,8 @@ private:
 	
 	void printData(string label);
 	vector<string> outputNames;
+    
+    int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 };
 
 #endif