working on pam

[mothur.git] / treereader.h

diff --git a/treereader.h b/treereader.h
index fb9c791959f96cd04ce95fae0385f02c9740f546..ac24eb0161336e3be68ad17028a2b6a28eab8489 100644 (file)
--- a/treereader.h
+++ b/treereader.h
@@ -11,29 +11,26 @@
 
 #include "mothurout.h"
 #include "tree.h"
+#include "counttable.h"
 
 class TreeReader {
     
 public:
     
-    TreeReader(string tf);
-       TreeReader(string tf, string gf);
+    TreeReader(string tf, string cf);
     TreeReader(string tf, string gf, string nf);
        ~TreeReader() {}        
     
     vector<Tree*> getTrees()            { return trees;     }
-    map<string, string> getNames()      { return nameMap;   } //dups -> unique
-    map<string, string> getNameMap()    { return names;     } //unique -> dups list
-    
     
 private:
     MothurOut* m;
        vector<Tree*> trees;
-    TreeMap* tmap;
-    map<string, string> nameMap; //dupName -> uniqueName
-    map<string, string> names;
+    CountTable* ct;
+    //map<string, string> nameMap; //dupName -> uniqueName
+   // map<string, string> names;
     
-    string treefile, groupfile, namefile;
+    string treefile, groupfile, namefile, countfile;
     
     bool readTrees();
     int readNamesFile();