X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=suffixtree.hpp;fp=suffixtree.hpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=d2b69e42325777d508a23000b0bc0924e0cc34f9;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/suffixtree.hpp b/suffixtree.hpp
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-#ifndef SUFFIXTREE_H
-#define SUFFIXTREE_H
-
-/*
- *  suffixtree.h
- *  
- *
- *  Created by Pat Schloss on 12/15/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *	This is my half-assed attempt to implement a suffix tree.  This is a cobbled together algorithm using materials that
- *	I found at http://marknelson.us/1996/08/01/suffix-trees/ and:
- *
- *		Ukkonen E. (1995). On-line construction of suffix trees. Algorithmica 14 (3): 249--260
- *		Gusfield, Dan (1999). Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. 
- *			USA: Cambridge University Press
- *
- *	The Ukkonen paper is the seminal paper describing the on-line method of constructing a suffix tree.
- *
- *	I have chosen to store the nodes of the tree as a vector of pointers to SuffixNode objects.  The root is stored at
- *	nodeVector[0].  Each tree also stores the sequence name and the string that corresponds to the actual sequence. 
- *	Finally, this class provides a way of counting the number of suffixes that are needed in one tree to generate a new
- *	sequence (countSuffixes).  This method is used to determine similarity between sequences and was inspired by the
- *	article and Perl source code provided at http://www.ddj.com/web-development/184416093.
- *
- */
-
-#include "mothur.h"
-
-class SuffixNode;
-
-//********************************************************************************************************************
-
-class SuffixTree {
-	
-public:
-	SuffixTree();
-	~SuffixTree();
-
-	void loadSequence(Sequence);
-	string getSeqName();
-	void print();	
-	int countSuffixes(string, int&);
-	int countSuffixes(string);	
-
-private:	
-	void addPrefix(int);
-	void canonize();
-	int split(int, int);
-	void makeSuffixLink(int&, int);
-	bool isExplicit(){	return activeStartPosition > activeEndPosition;	}
-	
-	int activeStartPosition;
-	int activeEndPosition;
-	
-	vector<SuffixNode*> nodeVector;
-	int root;
-	int activeNode;
-	int nodeCounter;
-	string seqName;
-	string sequence;
-	MothurOut* m;
-	
-};
-
-//********************************************************************************************************************
-
-#endif