added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / consensuscommand.h

diff --git a/consensuscommand.h b/consensuscommand.h
index 7a7960708c9b5d17d69355caaf8cfd8be089e76d..a9878517db3b6a1e1bc86d057f1ce5d6a2554b82 100644 (file)
--- a/consensuscommand.h
+++ b/consensuscommand.h
@@ -13,19 +13,26 @@
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
-       
-class GlobalData;
 
 class ConcensusCommand : public Command {
        
 public:
        ConcensusCommand(string);       
-       ~ConcensusCommand();
-       int execute();
-       void help();    
+       ConcensusCommand();
+       ~ConcensusCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "consensus";   }
+       string getCommandCategory()             { return "Hidden";              }
+       string getHelpString(); 
+       string getCitation() { return "no citation"; }
+       string getDescription()         { return "consensus"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
        SharedUtil* util;
        vector<Tree*> t;
        Tree* consensusTree;
@@ -43,6 +50,7 @@ private:
        string outputFile, notIncluded, filename;
        ofstream out, out2;
        int numNodes, numLeaves, count;  //count is the next available spot in the tree vector
+       vector<string> outputNames;
                                                                                
        int getSets();
        int getSubgroupRating(vector<string>);