broke up globaldata and moved error checking and help into commands

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 989c699c877ead1e27ea20a1c59a53a901bfa71a..76124f5f7ff3cb2d312eac3091ec1d7b2c727d03 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -34,9 +34,10 @@ typedef list<PCell>::iterator MatData;
 class TreeGroupCommand : public Command {
        
 public:
-       TreeGroupCommand();     
+       TreeGroupCommand(string);       
        ~TreeGroupCommand();
        int execute();  
+       void help();
        
 private:
        void createTree();
@@ -63,8 +64,19 @@ private:
        int numGroups;
        ofstream out;
        float precision, cutoff;
+       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 phylipfile, columnfile, namefile, calc, groups, line, label;
+       vector<string>  Estimators, Groups; //holds estimators to be used
+       
        //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
        void process(vector<SharedRAbundVector*>);
+       
+       
 
 };