X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarycommand.h;h=891d1570e3e55fd24f4d58260c023924584d7756;hp=1d93a333a8c971458ced6ca8803cb0b2027a48b2;hb=d1faab5efe1c28700890bdec5b4d8e817fa1dab2;hpb=050e1297eaf24fabbbe0e9b76c3a5acfb90eed7d

diff --git a/summarycommand.h b/summarycommand.h
index 1d93a33..891d157 100644
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -25,7 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "summary.single";			}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
 	string getDescription()		{ return "generate summary file that has the calculator value for each line in the OTU data"; }
 
@@ -37,7 +39,7 @@ private:
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
 	SAbundVector* sabund;
-	int abund, size, iters, subsampleSize;
+	int abund, size, iters, subsampleSize, alpha;
 
 	bool abort, allLines, groupMode, subsample;
 	set<string> labels; //holds labels to be used
@@ -48,7 +50,7 @@ private:
 	
 	vector<string> parseSharedFile(string);
 	vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
-    int process(SAbundVector*&, ofstream&, ofstream&, ofstream&);
+    int process(SAbundVector*&, ofstream&, ofstream&);
 
 
 };