working on pam

[mothur.git] / readtree.h

diff --git a/readtree.h b/readtree.h
index 6b074de839070a86bd3e010bbf222a7ec4011dce..8a692432c7cda431c6f5d73f409a0fa8e9152671 100644 (file)
--- a/readtree.h
+++ b/readtree.h
@@ -11,6 +11,7 @@
 
 #include "mothur.h"
 #include "tree.h"
+#include "counttable.h"
 
 #define MAX_LINE               513
 #define SKIPLINE(f,c)  {while((c=f.get())!=EOF && ((c) != '\n')){}}
@@ -24,17 +25,17 @@ class ReadTree {
                ReadTree(); 
                virtual ~ReadTree() {};
                
-               virtual int read(TreeMap*) = 0;
+               virtual int read(CountTable*) = 0;
                int readSpecialChar(istream&, char, string);
                int readNodeChar(istream& f);
                float readBranchLength(istream& f);
        
                vector<Tree*> getTrees() { return Trees; }
-               int AssembleTrees(map<string, string>);
+               int AssembleTrees();
                
        protected:
                vector<Tree*> Trees;
-               TreeMap* treeMap;
+               CountTable* ct;
                int numNodes, numLeaves;
                MothurOut* m;
                
@@ -48,13 +49,13 @@ class ReadNewickTree : public ReadTree {
 public:
        ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; } 
        ~ReadNewickTree() {};
-       int read(TreeMap*);
+       int read(CountTable*);
        
 private:
        Tree* T;
-       int readNewickInt(istream&, int&, Tree*, TreeMap*);
-       int readTreeString(TreeMap*);
-       string nexusTranslation(TreeMap*);
+       int readNewickInt(istream&, int&, Tree*, CountTable*);
+       int readTreeString(CountTable*);
+       string nexusTranslation(CountTable*);
        ifstream filehandle;
        string treeFile;
        string holder;