broke up globaldata and moved error checking and help into commands

[mothur.git] / readdistcommand.h

diff --git a/readdistcommand.h b/readdistcommand.h
index 981afa339308199105a0082c8458dd0b1ed7295c..b6e3ae44de298a115ce9a72de193b51ff951ea34 100644 (file)
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -26,9 +26,10 @@ class GlobalData;
 
 class ReadDistCommand : public Command {
 public:
-       ReadDistCommand();
+       ReadDistCommand(string);
        ~ReadDistCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -38,7 +39,13 @@ private:
        FullMatrix* matrix;
        GroupMap* groupMap;
        string filename, format, method;
+       string phylipfile, columnfile, namefile, groupfile;
        NameAssignment* nameMap;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort;
+
 };
 
 #endif