working on pam

[mothur.git] / venncommand.h

diff --git a/venncommand.h b/venncommand.h
index 9f369280fc66e53754da98a4b6252568a7960d90..4762902c51d4f1195e8f3fc604b1781ddb1df39f 100644 (file)
--- a/venncommand.h
+++ b/venncommand.h
@@ -25,8 +25,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "venn";                                        }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Venn"; }
        string getDescription()         { return "generates a Venn diagram from data provided in a shared file"; }
 
@@ -39,11 +40,11 @@ private:
        Venn* venn;
        vector<Calculator*> vennCalculators;    
        vector<SharedRAbundVector*> lookup;
-       set< set<int> > combosOfFour;
+       set< set<int> > combos;
        SAbundVector* sabund;
-       int abund, fontsize;
+       int abund, fontsize, perm;
        
-       bool abort, allLines, nseqs, perm;
+       bool abort, allLines, nseqs, sharedOtus;
        set<string> labels; //holds labels to be used
        string format, groups, calc, label, outputDir, sharedfile, listfile, inputfile;
        vector<string> Estimators, Groups, outputNames;