broke up globaldata and moved error checking and help into commands

[mothur.git] / getrabundcommand.h

diff --git a/getrabundcommand.h b/getrabundcommand.h
index 66a3211296edc7f2105af0ba2bfc10f85b7ae109..4b2c37f11340e8dfc940f549b2c97a7c8c339b38 100644 (file)
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -20,9 +20,10 @@ class GlobalData;
 
 class GetRAbundCommand : public Command {
 public:
-       GetRAbundCommand();
+       GetRAbundCommand(string);
        ~GetRAbundCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -32,6 +33,15 @@ private:
        InputData* input;
        ListVector* list;
        RAbundVector* rabund;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string line, label;
+
+       
 };
 
 #endif