broke up globaldata and moved error checking and help into commands

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index ad41a4506e926dc646066964ccdd11c98fc48826..37b9edb80224de6d7b7be0f722152e0bdd782b11 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -31,9 +31,10 @@ class GlobalData;
 class ClusterCommand : public Command {
        
 public:
-       ClusterCommand();       
+       ClusterCommand(string); 
        ~ClusterCommand();
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -43,7 +44,11 @@ private:
        RAbundVector* rabund;
        RAbundVector oldRAbund;
        ListVector oldList;
-       
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort;
+
        string method, fileroot, tag;
        double cutoff;
        int precision, length;