X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.h;h=f70bb322c76cd3bf897fd5498333e5da379557fd;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=7349961e252104c93cf26942d79b44f11ba7c0f5;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/clustercommand.h b/clustercommand.h
index 7349961..f70bb32 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.  
@@ -44,7 +45,7 @@ public:
 	
 private:
 	Cluster* cluster;
-	SparseMatrix* matrix;
+	SparseDistanceMatrix* matrix;
 	ListVector* list;
 	RAbundVector* rabund;
 	RAbundVector oldRAbund;
@@ -52,7 +53,7 @@ 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;
@@ -64,6 +65,8 @@ private:
 	
 	void printData(string label);
 	vector<string> outputNames;
+    
+    int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 };
 
 #endif