X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.h;h=6b074de839070a86bd3e010bbf222a7ec4011dce;hb=2ecee16fec29d4c525f740ec19b27962ca09c050;hp=d363cd6884835558fba84e9ebaad678c4efe21b5;hpb=60fdefb3a300b59c3bbeffdca8a5f1f30c6a43af;p=mothur.git

diff --git a/readtree.h b/readtree.h
index d363cd6..6b074de 100644
--- a/readtree.h
+++ b/readtree.h
@@ -9,11 +9,7 @@
  *
  */
 
-using namespace std;
-
-#include <string>
-#include <iostream>
-#include "globaldata.hpp"
+#include "mothur.h"
 #include "tree.h"
 
 #define MAX_LINE		513
@@ -26,21 +22,23 @@ class Tree;
 class ReadTree {
 	public:
 		ReadTree(); 
-		~ReadTree() {};
+		virtual ~ReadTree() {};
 		
-		virtual void read() {};
+		virtual int read(TreeMap*) = 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(map<string, string>);
 		
+	protected:
+		vector<Tree*> Trees;
+		TreeMap* treeMap;
 		int numNodes, numLeaves;
-		GlobalData* globaldata;
+		MothurOut* m;
+		
 		
-	protected:
-		Tree* T;
 };
 
 /****************************************************************************/
@@ -48,16 +46,22 @@ 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(TreeMap*);
 	
 private:
-	int readNewickInt(istream&, int&, Tree*);
+	Tree* T;
+	int readNewickInt(istream&, int&, Tree*, TreeMap*);
+	int readTreeString(TreeMap*);
+	string nexusTranslation(TreeMap*);
 	ifstream filehandle;
 	string treeFile;
+	string holder;
+	int readOk;  // readOk = 0 means success, readOk = 1 means errors.
+	
 };
 
 /****************************************************************************/
 
-#endif
\ No newline at end of file
+#endif