added shannonrange calc.

[mothur.git] / summarycommand.h

diff --git a/summarycommand.h b/summarycommand.h
index 1d93a333a8c971458ced6ca8803cb0b2027a48b2..891d1570e3e55fd24f4d58260c023924584d7756 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -25,7 +25,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "summary.single";                      }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
        string getDescription()         { return "generate summary file that has the calculator value for each line in the OTU data"; }
 
@@ -37,7 +39,7 @@ private:
        vector<Calculator*> sumCalculators;     
        InputData* input;
        SAbundVector* sabund;
-       int abund, size, iters, subsampleSize;
+       int abund, size, iters, subsampleSize, alpha;
 
        bool abort, allLines, groupMode, subsample;
        set<string> labels; //holds labels to be used
@@ -48,7 +50,7 @@ private:
        
        vector<string> parseSharedFile(string);
        vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
-    int process(SAbundVector*&, ofstream&, ofstream&, ofstream&);
+    int process(SAbundVector*&, ofstream&, ofstream&);
 
 
 };