X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarycommand.h;h=3c8420795550e1f39ef5529ad235d13e11e5e7a5;hp=1258c650179a73afd9bcc85e56bfee92dca1d996;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=92f998cc7debc4bf3e8594848586b8153d96db16

diff --git a/summarycommand.h b/summarycommand.h
index 1258c65..3c84207 100644
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -13,36 +13,44 @@
 #include "sabundvector.hpp"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
-class GlobalData;
-
 class SummaryCommand : public Command {
 
 public:
 	SummaryCommand(string);
-	~SummaryCommand();
-	int execute();
-	void help();
+	SummaryCommand();
+	~SummaryCommand(){}
+	
+	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()); }	
 	
 private:
-	GlobalData* globaldata;
-	ReadOTUFile* read;
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
-	ValidCalculators* validCalculator;
 	SAbundVector* sabund;
-	int abund, size;
+	int abund, size, iters, subsampleSize;
 
-	bool abort, allLines;
+	bool abort, allLines, groupMode, subsample;
 	set<string> labels; //holds labels to be used
-	string label, calc;
+	string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
 	vector<string>  Estimators;
-	vector<string> inputFileNames;
+	vector<string> inputFileNames, outputNames;
 	vector<string> groups;
 	
 	vector<string> parseSharedFile(string);
+	vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
+    int process(SAbundVector*&, ofstream&, ofstream&);
 
 
 };