moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
deleted file mode 100644 (file)
index a0baf18..0000000
--- a/classifyotucommand.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#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
-
-