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[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
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+#ifndef CLASSIFYOTUSCOMMAND_H
+#define CLASSIFYOTUSCOMMAND_H
+
+/*
+ *  classifyotucommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 6/1/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+#include "listvector.hpp"
+#include "inputdata.h"
+
+
+class ClassifyOtuCommand : public Command {
+
+public:
+       ClassifyOtuCommand(string);
+       ClassifyOtuCommand();
+       ~ClassifyOtuCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "classify.otu";                }
+       string getCommandCategory()             { return "Phylotype Analysis";  }
+       string getHelpString(); 
+       string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Classify.otu"; }
+       string getDescription()         { return "find the concensus taxonomy for each OTU"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+
+private:
+
+       ListVector* list;
+       InputData* input;
+       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
+       bool abort, allLines, probs;
+       int cutoff;
+       set<string> labels; //holds labels to be used
+       vector<string> outputNames;
+       map<string, string> nameMap;
+       map<string, string> taxMap;
+
+       int readNamesFile();
+       int readTaxonomyFile();
+       int process(ListVector*);
+       string addUnclassifieds(string, int);
+       vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&);  // returns the name of the "representative" taxonomy of given bin
+       
+                                                                                               
+};
+
+#endif
+
+