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

[mothur.git] / classifytreecommand.h

diff --git a/classifytreecommand.h b/classifytreecommand.h
index 758a438dc068f0790aab0b8b309f32a0fb6f24a5..dd972b61b457378462392f771d759585bef53188 100644 (file)
--- a/classifytreecommand.h
+++ b/classifytreecommand.h
@@ -12,6 +12,7 @@
 #include "command.hpp"
 #include "readtree.h"
 #include "treemap.h"
+#include "counttable.h"
 
 class ClassifyTreeCommand : public Command {
 public:
@@ -31,13 +32,14 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       string treefile, taxonomyfile, groupfile, namefile, outputDir;
+       string treefile, taxonomyfile, groupfile, namefile, countfile, outputDir;
        bool abort;
        vector<string> outputNames;
     int numUniquesInName, cutoff;
     map<string, string> nameMap;
     map<string, int> nameCount;
     map<string, string> taxMap;
+    CountTable* ct;
        
        int getClassifications(Tree*&);
        map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);