X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.h;h=7cfb4b426eef1ca38e562ae1c52b4ad240afc4e3;hb=c3396974063d6efc5e5850ddf4ed8ab65cc94bb9;hp=3df0e0a5f1312aaf3be2ee1f0c35bc5c93afb695;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/readtree.h b/readtree.h
index 3df0e0a..7cfb4b4 100644
--- a/readtree.h
+++ b/readtree.h
@@ -9,8 +9,6 @@
  *
  */
 
-using namespace std;
-
 #include "mothur.h"
 #include "globaldata.hpp"
 #include "tree.h"
@@ -25,7 +23,7 @@ class Tree;
 class ReadTree {
 	public:
 		ReadTree(); 
-		~ReadTree() {};
+		virtual ~ReadTree() {};
 		
 		virtual int read() = 0;
 		int readSpecialChar(istream&, char, string);
@@ -35,6 +33,7 @@ class ReadTree {
 	protected:
 		GlobalData* globaldata;
 		int numNodes, numLeaves;
+		MothurOut* m;
 		
 		
 };
@@ -44,7 +43,7 @@ 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();
 	
@@ -52,7 +51,7 @@ private:
 	Tree* T;
 	int readNewickInt(istream&, int&, Tree*);
 	int readTreeString();
-	void nexusTranslation();
+	string nexusTranslation();
 	ifstream filehandle;
 	string treeFile;
 	string holder;