X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarycommand.h;h=891d1570e3e55fd24f4d58260c023924584d7756;hp=5535237c98f97d32cacf3f967cb2501199a76473;hb=d1faab5efe1c28700890bdec5b4d8e817fa1dab2;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/summarycommand.h b/summarycommand.h
index 5535237..891d157 100644
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -25,7 +25,12 @@ 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"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -34,9 +39,9 @@ private:
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
 	SAbundVector* sabund;
-	int abund, size;
+	int abund, size, iters, subsampleSize, alpha;
 
-	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;
@@ -44,7 +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&);
 
 
 };