X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarycommand.h;h=3c8420795550e1f39ef5529ad235d13e11e5e7a5;hp=15b7f4066e9f17b263b30ac3d0b663d7cd414455;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf

diff --git a/summarycommand.h b/summarycommand.h
index 15b7f40..3c84207 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"; }
 
@@ -37,9 +39,9 @@ private:
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
 	SAbundVector* sabund;
-	int abund, size;
+	int abund, size, iters, subsampleSize;
 
-	bool abort, allLines, groupMode;
+	bool abort, allLines, groupMode, subsample;
 	set<string> labels; //holds labels to be used
 	string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
 	vector<string>  Estimators;
@@ -47,7 +49,8 @@ private:
 	vector<string> groups;
 	
 	vector<string> parseSharedFile(string);
-	string createGroupSummaryFile(int, int, vector<string>&);
+	vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
+    int process(SAbundVector*&, ofstream&, ofstream&);
 
 
 };