X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.h;h=6b074de839070a86bd3e010bbf222a7ec4011dce;hb=110ed3a070bf6b602cccef89c8626cce033315d3;hp=15597bafbfd64eb88c2f4304aff0fb9b78ac60ea;hpb=9651e8e7172d86707b34af15e95ec60ad4c3c3f9;p=mothur.git

diff --git a/readtree.h b/readtree.h
index 15597ba..6b074de 100644
--- a/readtree.h
+++ b/readtree.h
@@ -9,10 +9,7 @@
  *
  */
 
-using namespace std;
-
-#include "globaldata.hpp"
-#include "utilities.hpp"
+#include "mothur.h"
 #include "tree.h"
 
 #define MAX_LINE		513
@@ -25,16 +22,21 @@ class Tree;
 class ReadTree {
 	public:
 		ReadTree(); 
-		~ReadTree() {};
+		virtual ~ReadTree() {};
 		
-		virtual int read() = 0;
+		virtual int read(TreeMap*) = 0;
 		int readSpecialChar(istream&, char, string);
 		int readNodeChar(istream& f);
 		float readBranchLength(istream& f);
+	
+		vector<Tree*> getTrees() { return Trees; }
+		int AssembleTrees(map<string, string>);
 		
 	protected:
-		GlobalData* globaldata;
+		vector<Tree*> Trees;
+		TreeMap* treeMap;
 		int numNodes, numLeaves;
+		MothurOut* m;
 		
 		
 };
@@ -44,15 +46,15 @@ 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(TreeMap*);
 	
 private:
 	Tree* T;
-	int readNewickInt(istream&, int&, Tree*);
-	int readTreeString();
-	void nexusTranslation();
+	int readNewickInt(istream&, int&, Tree*, TreeMap*);
+	int readTreeString(TreeMap*);
+	string nexusTranslation(TreeMap*);
 	ifstream filehandle;
 	string treeFile;
 	string holder;