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

[mothur.git] / classify.h

diff --git a/classify.h b/classify.h
deleted file mode 100644 (file)
index 4e03547..0000000
--- a/classify.h
+++ /dev/null
@@ -1,60 +0,0 @@
-#ifndef CLASSIFY_H
-#define CLASSIFY_H
-
-/*
- *  classify.h
- *  Mothur
- *
- *  Created by westcott on 11/3/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-
-/* This class is a parent to bayesian, knn.  */
-
-#include "mothur.h"
-#include "database.hpp"
-#include "phylotree.h"
-
-
-class Sequence;
-
-
-/**************************************************************************************************/
-
-class Classify {
-
-public:
-       Classify();
-       virtual ~Classify(){};
-       virtual string getTaxonomy(Sequence*) = 0;
-       virtual string getSimpleTax()  { return simpleTax;      }
-       virtual bool getFlipped()  { return flipped;    }
-       virtual void generateDatabaseAndNames(string, string, string, int, float, float, float, float);
-       virtual void setDistName(string s) {} //for knn, so if distance method is selected with knn you can create the smallest distance file in the right place.
-       
-protected:
-
-       map<string, string> taxonomy;  //name maps to taxonomy
-       //map<string, int> genusCount;  //maps genus to count - in essence a list of how many seqs are in each taxonomy
-       map<string, int>::iterator itTax;
-       map<string, string>::iterator it;
-       Database* database;
-       PhyloTree* phyloTree;
-       
-       string taxFile, templateFile, simpleTax;
-       vector<string> names;
-       int threadID;
-       bool flip, flipped;
-       
-       int readTaxonomy(string);
-       vector<string> parseTax(string);
-       MothurOut* m;
-       
-};
-
-/**************************************************************************************************/
-
-#endif
-