broke up globaldata and moved error checking and help into commands

[mothur.git] / concensuscommand.h

diff --git a/concensuscommand.h b/concensuscommand.h
index cc923dd34fde054ea38f7797ac4c3dee64cb1346..970102ac27f7a15e6dbfe7b0db2370129861aff3 100644 (file)
--- a/concensuscommand.h
+++ b/concensuscommand.h
@@ -19,15 +19,17 @@ class GlobalData;
 class ConcensusCommand : public Command {
        
 public:
-       ConcensusCommand();     
+       ConcensusCommand(string);       
        ~ConcensusCommand();
-       int execute();  
+       int execute();
+       void help();    
        
 private:
        GlobalData* globaldata;
        SharedUtil* util;
        vector<Tree*> t;
        Tree* concensusTree;
+       bool abort;
        vector<string> treeSet;         //set containing all members of the tree to start recursion.  filled in getSets().
        map< vector<string>, int > nodePairs;  //<map of possible combinations these combos are the pcounts or descendants info, to how many times they occured
                                                                                // ie. combos FI and EGK would create nodePairs[vector containing F and I] = 1; nodePairs[vector containing E, G and K] = 1