added modify names parameter to set.dir

[mothur.git] / normalizesharedcommand.h

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
index 6332fd7fe1f36f19cd232cde99d9c6629fc00ca5..53bcd6b5e4aac7d0a463fa436fc8ed6346f5f069 100644 (file)
--- a/normalizesharedcommand.h
+++ b/normalizesharedcommand.h
@@ -24,8 +24,12 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "normalize.shared";            }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
+       string getDescription()         { return "normalize samples in a shared or relabund file"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -42,8 +46,8 @@ private:
        int norm;
        vector<string> Groups, outputNames;
                
-       int normalize(vector<SharedRAbundVector*>&, ofstream&);
-       int normalize(vector<SharedRAbundFloatVector*>&, ofstream&);
+       int normalize(vector<SharedRAbundVector*>&);
+       int normalize(vector<SharedRAbundFloatVector*>&);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
        int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);