working on pam

[mothur.git] / readtree.h

diff --git a/readtree.h b/readtree.h
index 15597bafbfd64eb88c2f4304aff0fb9b78ac60ea..8a692432c7cda431c6f5d73f409a0fa8e9152671 100644 (file)
--- a/readtree.h
+++ b/readtree.h
@@ -9,11 +9,9 @@
  *
  */
 
-using namespace std;
-
-#include "globaldata.hpp"
-#include "utilities.hpp"
+#include "mothur.h"
 #include "tree.h"
+#include "counttable.h"
 
 #define MAX_LINE               513
 #define SKIPLINE(f,c)  {while((c=f.get())!=EOF && ((c) != '\n')){}}
@@ -25,16 +23,21 @@ class Tree;
 class ReadTree {
        public:
                ReadTree(); 
-               ~ReadTree() {};
+               virtual ~ReadTree() {};
                
-               virtual int read() = 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();
                
        protected:
-               GlobalData* globaldata;
+               vector<Tree*> Trees;
+               CountTable* ct;
                int numNodes, numLeaves;
+               MothurOut* m;
                
                
 };
@@ -44,15 +47,15 @@ class ReadTree {
 class ReadNewickTree : public ReadTree {
        
 public:
-       ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle); readOk = 0; } 
+       ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; } 
        ~ReadNewickTree() {};
-       int read();
+       int read(CountTable*);
        
 private:
        Tree* T;
-       int readNewickInt(istream&, int&, Tree*);
-       int readTreeString();
-       void nexusTranslation();
+       int readNewickInt(istream&, int&, Tree*, CountTable*);
+       int readTreeString(CountTable*);
+       string nexusTranslation(CountTable*);
        ifstream filehandle;
        string treeFile;
        string holder;