X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.h;fp=classify.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=4e0354782e5063e2a52268e88a1412b40db3c28e;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/classify.h b/classify.h
deleted file mode 100644
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
-