X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readtree.h;h=8a692432c7cda431c6f5d73f409a0fa8e9152671;hp=1abef8a179478b9db980ee6c21e6e6b9855a024b;hb=615301e57c25e241356a9c2380648d117709458d;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed

diff --git a/readtree.h b/readtree.h
index 1abef8a..8a69243 100644
--- a/readtree.h
+++ b/readtree.h
@@ -9,12 +9,9 @@
  *
  */
 
-using namespace std;
-
-#include <string>
-#include <iostream>
-#include "globaldata.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')){}}
@@ -26,21 +23,23 @@ class Tree;
 class ReadTree {
 	public:
 		ReadTree(); 
-		~ReadTree() {};
+		virtual ~ReadTree() {};
 		
-		virtual void read() {};
+		virtual int read(CountTable*) = 0;
 		int readSpecialChar(istream&, char, string);
 		int readNodeChar(istream& f);
 		float readBranchLength(istream& f);
-
-				
-		Tree* getTree()  { return T; }
+	
+		vector<Tree*> getTrees() { return Trees; }
+		int AssembleTrees();
 		
+	protected:
+		vector<Tree*> Trees;
+		CountTable* ct;
 		int numNodes, numLeaves;
-		GlobalData* globaldata;
+		MothurOut* m;
+		
 		
-	protected:
-		Tree* T;
 };
 
 /****************************************************************************/
@@ -48,14 +47,20 @@ class ReadTree {
 class ReadNewickTree : public ReadTree {
 	
 public:
-	ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle); }
+	ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; } 
 	~ReadNewickTree() {};
-	void read();
+	int read(CountTable*);
 	
 private:
-	int readNewickInt(istream&, int&, Tree*);
+	Tree* T;
+	int readNewickInt(istream&, int&, Tree*, CountTable*);
+	int readTreeString(CountTable*);
+	string nexusTranslation(CountTable*);
 	ifstream filehandle;
 	string treeFile;
+	string holder;
+	int readOk;  // readOk = 0 means success, readOk = 1 means errors.
+	
 };
 
 /****************************************************************************/