added filter.shared command. fixed lci and uci for thetayc calc

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 7342b36584ce76b3b22a96d0e3ba885cb2ab172a..979612f4aea3aa41187ea520483afadfa05b1782 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -78,8 +78,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "tree.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
        string getDescription()         { return "generate a tree file that describes the dissimilarity among groups"; }
 
@@ -110,7 +111,7 @@ private:
        vector<Calculator*> treeCalculators;
        vector<SharedRAbundVector*> lookup;
        string lastLabel;
-       string format, groupNames, filename, sharedfile, inputfile;
+       string format, groupNames, filename, sharedfile, countfile, inputfile;
        int numGroups, subsampleSize, iters, processors;
        ofstream out;
        float precision, cutoff;