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[mothur.git] / 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