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[mothur.git] / collectcommand.h

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+#ifndef COLLECTCOMMAND_H
+#define COLLECTCOMMAND_H
+/*
+ *  collectcommand.h
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "ordervector.hpp"
+#include "inputdata.h"
+#include "collect.h"
+#include "display.h"
+#include "validcalculator.h"
+
+/*The collect() command:
+       The collect command generates a collector's curve from the given file.  
+       The collect command outputs a file for each estimator you choose to use.  The collect command parameters are label, freq, single, abund.  
+       No parameters are required.  
+       The collect command should be in the following format: collect(label=yourLabel, freq=yourFreq, single=yourEstimators, abund=yourAbund). 
+       example collect(label=unique-.01-.03, freq=10, single=collect-chao-ace-jack).  
+       The default values for  freq is 100, for abund is 10, and single are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.  
+       The valid single estimators are: collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson. 
+       The label parameter is used to analyze specific labels in your input. */
+
+
+class CollectCommand : public Command {
+       
+public:
+       CollectCommand(string); 
+       CollectCommand();
+       ~CollectCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "collect.single";                      }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       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.single"; }
+       string getHelpString(); 
+       string getDescription()         { return "generates collector's curves using calculators, that describe the richness, diversity, and other features of individual samples"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       OrderVector* order;
+       InputData* input;
+       Collect* cCurve;
+       vector<Display*> cDisplays;
+       int abund, size;
+       float freq;
+       vector<string> outputNames;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
+       vector<string>  Estimators;
+       vector<string> inputFileNames;
+       vector<string> groups;
+       
+       vector<string> parseSharedFile(string);
+
+
+};
+
+#endif