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[mothur.git] / collectsharedcommand.h

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+#ifndef COLLECTSHAREDCOMMAND_H
+#define COLLECTSHAREDCOMMAND_H
+/*
+ *  collectsharedcommand.h
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "sharedordervector.h"
+#include "inputdata.h"
+#include "collect.h"
+#include "display.h"
+#include "validcalculator.h"
+#include "sharedutilities.h"
+
+
+class CollectSharedCommand : public Command {
+       
+public:
+       CollectSharedCommand(string);   
+       CollectSharedCommand(); 
+       ~CollectSharedCommand();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "collect.shared";                      }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.shared"; }
+       string getDescription()         { return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       SharedOrderVector* order;
+       InputData* input;
+       Collect* cCurve;
+       vector<Display*> cDisplays;
+       float freq;
+
+       bool abort, allLines, all;
+       set<string> labels; //holds labels to be used
+       string label, calc, groups, outputDir, sharedfile;
+       vector<string>  Estimators, Groups, outputNames;
+};
+
+#endif