X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;h=b5b295f1edb4495d321a7e614db1e8309d8bc481;hb=cc19310422f125d6628980bd1148e1e816792382;hp=96410bfc39f1a28140357cdf2ee9233fe5e51bc2;hpb=13f0aaa1f941bb5c066e626331549fa177810732;p=mothur.git

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 96410bf..b5b295f 100644
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -12,12 +12,12 @@
 
 #include "command.hpp"
 #include "readblast.h"
-#include "sparsematrix.hpp"
 #include "nameassignment.hpp"
 #include "cluster.hpp"
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
+#include "counttable.h"
 
 /**********************************************************************/
 
@@ -46,23 +46,24 @@ private:
 	Cluster* cluster;
 	HCluster* hcluster;
 	ListVector* list;
+    CountTable* ct;
 	ListVector oldList;
-        RAbundVector rav;
+    RAbundVector rav;
 	vector<seqDist> overlapMatrix;
 	vector<string> outputNames;
 	
-	string blastfile, method, namefile, overlapFile, distFile, outputDir;
+	string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
 	ofstream sabundFile, rabundFile, listFile;
 	double cutoff;
 	float penalty;
 	int precision, length, precisionLength;
-	bool abort, minWanted, hclusterWanted, merge, hard, large;
+	bool abort, minWanted, hclusterWanted, merge, hard;
 	
 	void printData(ListVector*);
 	ListVector* mergeOPFs(map<string, int>, float);
 	void sortHclusterFiles(string, string);
 	vector<seqDist> getSeqs(ifstream&);
-        void createRabund(map<string, int>);
+    void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
 
 };