broke up globaldata and moved error checking and help into commands

[mothur.git] / bootstrapsharedcommand.h

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index b632acede61e9f06c576ea236e7eac4b7c896153..9ff44b377ab90472b8bb5867a9e5bb9a18208068 100644 (file)
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -25,9 +25,10 @@ class GlobalData;
 class BootSharedCommand : public Command {
        
 public:
-       BootSharedCommand();    
+       BootSharedCommand(string);      
        ~BootSharedCommand();
        int execute();  
+       void help();
        
 private:
        void createTree(ostream*);
@@ -48,8 +49,15 @@ private:
        ValidCalculators* validCalculator;
        SharedOrderVector* order;
        vector<SharedRAbundVector*> lookup;
-       string format, outputFile;
+       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 outputFile, calc, groups, line, label;
        int numGroups, iters;
+       vector<string>  Estimators, Groups; //holds estimators to be used
 
 };