X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=otuassociationcommand.h;h=e9cdb2a290fb5a778bf936e3040b97433121be32;hp=7aaa88a61c37a21ec6a9af5d1bb8f0c90066c222;hb=615301e57c25e241356a9c2380648d117709458d;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/otuassociationcommand.h b/otuassociationcommand.h
index 7aaa88a..e9cdb2a 100644
--- a/otuassociationcommand.h
+++ b/otuassociationcommand.h
@@ -25,7 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "otu.association";			}
 	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	
 	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"; }
 	
@@ -33,15 +35,20 @@ public:
 	void help() { m->mothurOut(getHelpString()); }	
 private:
 	
-	string sharedfile, relabundfile, groups, label, inputFileName, outputDir, method;
+	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;
 	
-	vector<string> outputNames, Groups;
+	vector<string> outputNames, Groups, metadataLabels;
 	int processShared();
 	int process(vector<SharedRAbundVector*>&);
 	int processRelabund();
 	int process(vector<SharedRAbundFloatVector*>&);
+    int readMetadata();
+    int getMetadata();
 	
 };