X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clustercommand.h;h=96b7c08861f216862de0c1e600d07fed463eb56a;hp=268ec315a81e1bbbcbd80051986703f3e02f03d4;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/clustercommand.h b/clustercommand.h
index 268ec31..96b7c08 100644
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -14,7 +14,8 @@
 #include "sabundvector.hpp"
 #include "listvector.hpp"
 #include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
+#include "counttable.h"
 
 /* The cluster() command:
 	The cluster command outputs a .list , .rabund and .sabund files.  
@@ -34,8 +35,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "cluster";		}
 	string getCommandCategory()		{ return "Clustering";	}
+	
 	string getHelpString();	
-	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. \nhttp://www.mothur.org/wiki/Cluster"; }
+    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(); 
@@ -43,7 +46,7 @@ public:
 	
 private:
 	Cluster* cluster;
-	SparseMatrix* matrix;
+	SparseDistanceMatrix* matrix;
 	ListVector* list;
 	RAbundVector* rabund;
 	RAbundVector oldRAbund;
@@ -51,7 +54,7 @@ private:
 
 	bool abort, hard, sim;
 
-	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile;
+	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
 	double cutoff;
 	string showabund, timing;
 	int precision, length;
@@ -63,6 +66,8 @@ private:
 	
 	void printData(string label);
 	vector<string> outputNames;
+    
+    int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 };
 
 #endif