removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / consensuscommand.h

diff --git a/consensuscommand.h b/consensuscommand.h
index d5072da082cd020d1836e39c06228fa4689eafbe..6bd5d3e0edffe82be92d116fcacfe1c0c94a3173 100644 (file)
--- a/consensuscommand.h
+++ b/consensuscommand.h
@@ -13,24 +13,24 @@
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
-       
-class GlobalData;
 
 class ConcensusCommand : public Command {
        
 public:
        ConcensusCommand(string);       
        ConcensusCommand();
-       ~ConcensusCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       ~ConcensusCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "concensus";   }
+       string getCommandCategory()             { return "Hidden";              }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
        SharedUtil* util;
        vector<Tree*> t;
        Tree* consensusTree;
@@ -49,7 +49,6 @@ private:
        ofstream out, out2;
        int numNodes, numLeaves, count;  //count is the next available spot in the tree vector
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
                                                                                
        int getSets();
        int getSubgroupRating(vector<string>);