broke up globaldata and moved error checking and help into commands

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index 7c5ec4278bf75e95043b28ea68eda32e54b17837..3b79d7f2144c0c41c6b42f221bd53d2a6dfe07aa 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -37,9 +37,10 @@ class GlobalData;
 class CollectCommand : public Command {
        
 public:
-       CollectCommand();       
+       CollectCommand(string); 
        ~CollectCommand();
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -51,6 +52,15 @@ private:
        ValidCalculators* validCalculator;
        vector<Display*> cDisplays;
        int freq, abund, size;
+       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, calc;
+       vector<string>  Estimators;
+
 
 };