X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.h;h=464a825d002e7e1ac3cfe7f43af91142d2a6aeb9;hb=4f9a6e14a608172f8a97f0297a3b8e6ea267c518;hp=2ee72a15e591374d1df21a4aed7ff2f6a0457cde;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/readtreecommand.h b/readtreecommand.h
index 2ee72a1..464a825 100644
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -18,15 +18,29 @@ class GlobalData;
 
 class ReadTreeCommand : public Command {
 public:
-	ReadTreeCommand();
+	ReadTreeCommand(string);
+	ReadTreeCommand() { abort = true; calledHelp = true; }
 	~ReadTreeCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
 	ReadTree* read;
 	TreeMap* treeMap;
-	string filename;
+	string filename, treefile, groupfile, namefile;
+	bool abort;
+	map<string, string> nameMap;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
+	
+	int readNamesFile();
+	int numUniquesInName;
+
 };