X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=otuassociationcommand.h;h=e9cdb2a290fb5a778bf936e3040b97433121be32;hp=64995ac38e146ff6994ab17f624e329fd848cd57;hb=615301e57c25e241356a9c2380648d117709458d;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/otuassociationcommand.h b/otuassociationcommand.h
index 64995ac..e9cdb2a 100644
--- 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;