changing command name classify.shared to classifyrf.shared

[mothur.git] / otuassociationcommand.h

diff --git a/otuassociationcommand.h b/otuassociationcommand.h
index 64995ac38e146ff6994ab17f624e329fd848cd57..e9cdb2a290fb5a778bf936e3040b97433121be32 100644 (file)
--- a/otuassociationcommand.h
+++ b/otuassociationcommand.h
@@ -25,8 +25,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "otu.association";                     }
        string getCommandCategory()             { return "Hypothesis Testing";          }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Otu.association"; }
        string getDescription()         { return "calculate the correlation coefficient for the otus in a shared/relabund file"; }
        
@@ -36,6 +37,7 @@ private:
        
        string sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
        bool abort, pickedGroups, allLines;
+    double cutoff;
        set<string> labels;
     vector<SharedRAbundFloatVector*> metadataLookup;
     vector< vector< double> > metadata;