X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readtree.h;h=8a692432c7cda431c6f5d73f409a0fa8e9152671;hp=6b074de839070a86bd3e010bbf222a7ec4011dce;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=f55cf350ca6643f8eb070d8336e1957699a3f109

diff --git a/readtree.h b/readtree.h
index 6b074de..8a69243 100644
--- a/readtree.h
+++ b/readtree.h
@@ -11,6 +11,7 @@
 
 #include "mothur.h"
 #include "tree.h"
+#include "counttable.h"
 
 #define MAX_LINE		513
 #define SKIPLINE(f,c)	{while((c=f.get())!=EOF && ((c) != '\n')){}}
@@ -24,17 +25,17 @@ class ReadTree {
 		ReadTree(); 
 		virtual ~ReadTree() {};
 		
-		virtual int read(TreeMap*) = 0;
+		virtual int read(CountTable*) = 0;
 		int readSpecialChar(istream&, char, string);
 		int readNodeChar(istream& f);
 		float readBranchLength(istream& f);
 	
 		vector<Tree*> getTrees() { return Trees; }
-		int AssembleTrees(map<string, string>);
+		int AssembleTrees();
 		
 	protected:
 		vector<Tree*> Trees;
-		TreeMap* treeMap;
+		CountTable* ct;
 		int numNodes, numLeaves;
 		MothurOut* m;
 		
@@ -48,13 +49,13 @@ class ReadNewickTree : public ReadTree {
 public:
 	ReadNewickTree(string file) : treeFile(file) { m->openInputFile(file, filehandle); readOk = 0; } 
 	~ReadNewickTree() {};
-	int read(TreeMap*);
+	int read(CountTable*);
 	
 private:
 	Tree* T;
-	int readNewickInt(istream&, int&, Tree*, TreeMap*);
-	int readTreeString(TreeMap*);
-	string nexusTranslation(TreeMap*);
+	int readNewickInt(istream&, int&, Tree*, CountTable*);
+	int readTreeString(CountTable*);
+	string nexusTranslation(CountTable*);
 	ifstream filehandle;
 	string treeFile;
 	string holder;