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

[mothur.git] / suffixdb.hpp

diff --git a/suffixdb.hpp b/suffixdb.hpp
deleted file mode 100644 (file)
index 3796801..0000000
--- a/suffixdb.hpp
+++ /dev/null
@@ -1,41 +0,0 @@
-#ifndef SUFFIXDB_HPP
-#define SUFFIXDB_HPP
-
-/*
- *  suffixdb.hpp
- *  
- *
- *  Created by Pat Schloss on 12/16/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *     This is a child class of the Database abstract datatype.  The class is basically a database of suffix trees and an
- *     encapsulation of the method for finding the most similar tree to an inputted sequence.  the suffixForest object
- *     is a vector of SuffixTrees, with each template sequence being represented by a different SuffixTree.  The class also
- *     provides a method to take an unaligned sequence and find the closest sequence in the suffixForest.  The search
- *     method is inspired by the article and Perl source code provided at http://www.ddj.com/web-development/184416093.  I 
- *     would estimate that the time complexity is O(LN) for each search, which is slower than the kmer searching, but 
- *     faster than blast
- *
- */
-
-#include "mothur.h"
-#include "database.hpp"
-#include "suffixtree.hpp"
-
-class SuffixDB : public Database {
-       
-public:
-       SuffixDB(int);
-       SuffixDB();
-       ~SuffixDB();
-       
-       void generateDB() {}; //adding sequences generates the db
-       void addSequence(Sequence);
-       vector<int> findClosestSequences(Sequence*, int);
-
-private:
-       vector<SuffixTree> suffixForest;
-       int count;
-};
-
-#endif