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

[mothur.git] / suffixtree.hpp

diff --git a/suffixtree.hpp b/suffixtree.hpp
deleted file mode 100644 (file)
index d2b69e4..0000000
--- a/suffixtree.hpp
+++ /dev/null
@@ -1,68 +0,0 @@
-#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