broke up globaldata and moved error checking and help into commands

[mothur.git] / readtreecommand.h

diff --git a/readtreecommand.h b/readtreecommand.h
index 2ee72a15e591374d1df21a4aed7ff2f6a0457cde..ca9f3b8c581d7b72f277332a1b70936d9f095854 100644 (file)
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -18,15 +18,21 @@ class GlobalData;
 
 class ReadTreeCommand : public Command {
 public:
-       ReadTreeCommand();
+       ReadTreeCommand(string);
        ~ReadTreeCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
        ReadTree* read;
        TreeMap* treeMap;
-       string filename;
+       string filename, treefile, groupfile;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort;
+
 };