X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.h;h=cbf376909ff998531ed959f34edb5d72e8b72fcd;hb=133dddf9ffde5059e3ea8290a2e7742843e3f2b7;hp=e9424b2be6d534c61dca64195e2272d7782e0aa4;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/readtreecommand.h b/readtreecommand.h
index e9424b2..cbf3769 100644
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -10,25 +10,38 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "readtree.h"
 #include "treemap.h"
 
-class GlobalData;
 
 class ReadTreeCommand : public Command {
 public:
-	ReadTreeCommand();
-	~ReadTreeCommand();
-	int execute();
+	ReadTreeCommand(string);
+	ReadTreeCommand() { abort = true; calledHelp = true; }
+	~ReadTreeCommand() {}
+	
+	vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
+	string getCommandName()			{ return "read.tree";	}
+	string getCommandCategory()		{ return "Hidden";	}
+	string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like unifrac.unweighted."; }	
+	string getCitation() { return "http://www.mothur.org/wiki/Read.tree"; }
+	string getDescription()		{ return "read.tree"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
 	ReadTree* read;
 	TreeMap* treeMap;
-	string filename;
+	string filename, treefile, groupfile, namefile;
+	bool abort;
+	map<string, string> nameMap;
+	vector<string> outputNames;
+	
+	int readNamesFile();
+	int numUniquesInName;
+
 };