major change to the tree class to use the count table class instead of tree map....

[mothur.git] / clusterfragmentscommand.h

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index c322529f3bedf95600a8b30e0ac013be2870d290..e3d861a8a1477c0edf71ae7208c86560ceb56860 100644 (file)
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "sequence.hpp"
+#include "counttable.h"
 
 /************************************************************/
 struct seqRNode {
@@ -46,8 +47,9 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
+    CountTable ct;
        bool abort;
-       string fastafile, namefile, outputDir;
+       string fastafile, namefile, countfile, outputDir;
        int diffs, percent;
        vector<seqRNode> alignSeqs; 
        map<string, string> names; //represents the names file first column maps to second column