broke up globaldata and moved error checking and help into commands

[mothur.git] / getsabundcommand.h

diff --git a/getsabundcommand.h b/getsabundcommand.h
index 27d25c2f2c3d2739bb6cfecd85f7b059b4867442..cd95d94e915f53d947e37b12127b898d65d43fd8 100644 (file)
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -20,9 +20,10 @@ class GlobalData;
 
 class GetSAbundCommand : public Command {
 public:
-       GetSAbundCommand();
+       GetSAbundCommand(string);
        ~GetSAbundCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -33,6 +34,14 @@ private:
        OrderVector* lastOrder;
        InputData* input;
        SAbundVector* sabund;
+       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