X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.h;fp=summarycommand.h;h=15b7f4066e9f17b263b30ac3d0b663d7cd414455;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/summarycommand.h b/summarycommand.h
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+#ifndef SUMMARYCOMMAND_H
+#define SUMMARYCOMMAND_H
+/*
+ *  summarycommand.h
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "sabundvector.hpp"
+#include "inputdata.h"
+#include "calculator.h"
+#include "validcalculator.h"
+
+class SummaryCommand : public Command {
+
+public:
+	SummaryCommand(string);
+	SummaryCommand();
+	~SummaryCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "summary.single";			}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	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:
+	vector<Calculator*> sumCalculators;	
+	InputData* input;
+	SAbundVector* sabund;
+	int abund, size;
+
+	bool abort, allLines, groupMode;
+	set<string> labels; //holds labels to be used
+	string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
+	vector<string>  Estimators;
+	vector<string> inputFileNames, outputNames;
+	vector<string> groups;
+	
+	vector<string> parseSharedFile(string);
+	string createGroupSummaryFile(int, int, vector<string>&);
+
+
+};
+#endif