X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readtree.h;h=8a692432c7cda431c6f5d73f409a0fa8e9152671;hp=41d03058d6478cb371737dbc385c8bb5d0a1c999;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1

diff --git a/readtree.h b/readtree.h
index 41d0305..8a69243 100644
--- a/readtree.h
+++ b/readtree.h
@@ -9,22 +9,60 @@
  *
  */
 
-using namespace std;
+#include "mothur.h"
+#include "tree.h"
+#include "counttable.h"
 
-#include <string>
-#include <iostream>
+#define MAX_LINE		513
+#define SKIPLINE(f,c)	{while((c=f.get())!=EOF && ((c) != '\n')){}}
 
+class Tree;
+
+/****************************************************************************/
 
 class ReadTree {
 	public:
-		ReadTree();
-		~ReadTree();
+		ReadTree(); 
+		virtual ~ReadTree() {};
 		
+		virtual int read(CountTable*) = 0;
+		int readSpecialChar(istream&, char, string);
+		int readNodeChar(istream& f);
+		float readBranchLength(istream& f);
 	
-	private:
-	
+		vector<Tree*> getTrees() { return Trees; }
+		int AssembleTrees();
+		
+	protected:
+		vector<Tree*> Trees;
+		CountTable* ct;
+		int numNodes, numLeaves;
+		MothurOut* m;
+		
+		
+};
+
+/****************************************************************************/
 
+class ReadNewickTree : public ReadTree {
+	
+public:
+	ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; } 
+	~ReadNewickTree() {};
+	int read(CountTable*);
+	
+private:
+	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.
+	
 };
 
+/****************************************************************************/
 
-#endif
\ No newline at end of file
+#endif