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Title: Algorithms/Sorting and Searching - Suffix Tree ANSI C implementation of E. Ukkonen's algorithm that makes it convenient to do string matching against a data set in O(N) time. Includes source code, an interface in Perl, and a write-up.
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ANSI C implementation of a Suffix Tree

ANSI C implementation of a Suffix Tree

What you will find in this page

You can view and download an ANSI C implementation of a suffix tree. You can view and download a Perl Module that interfaces the ANSI-C implementation of the suffix tree so you can easily use the functionality under Perl as well. You can check out links to ports and wrappers to this code to different programming languages.

The Suffix Tree data structure

A suffix tree is a data structure that exposes the internal structure of a string in a deep way, and can be used to solve the exact matching problem in linear time, but its real virtue comes from its use in linear-time solutions to many string problems more complex than exact string matching. The following definitions are taken from [1], which contains conprehensive overview of the suffix tree data structure: Definition A suffix tree T for an m-character string S is a rooted directed tree with exactly m leaves numbered 1 to m. Each internal node, other than the root, has at least two children and each edge is labeled with a nonempty substring of S. No two edges out of a node can have edge-labels beginning with the same character. The key feature of the suffix tree is that for any leaf i, the concatenation of the edge-labels on the path from the root to leaf i exactly spells out the suffix of S that starts at position i. That is, it spells out S[i..m].

Authors and maintainers

The source code was initially by Dotan Tsadok who worked (on and off) on it from 24.12.2001 untill 21.8.2002 as his undergraduate project in Haifa university. The current maintainer is Shlomo Yona. A Perl interface for this suffix tree data structure is available thanks to Offer Kaye, with whom I produced the first working version.

TODO

Put everyting into a CVS repository. Slight rewrites to code and documentation so they look nice. Intensive testing. Support alphabets from very small (e.g. the 'A','C','G','T' alphabet from biology) to very large (e.g. Chinese alphabet). Current version supports alphabets with no more than 255 characters, and is not memory efficient with very small alphabets (which can be more efficiently treated using bitwise operators). Enhance the general robustness and scalability of the implementation. Supply several toy examples for uses of the suffix tree. Supply several real world examples for uses of the suffix tree. Supply interfaces to this code under more languages (e.g. Java, Python).

Compilation

Under Linux one would probably do something like this: make Makefile

Files

Project report summary README. The original project report Dotan wrote project_report.rtf. The header file suffix_tree.h. The implementation file suffix_tree.c. A simple example of using the code as through the interface as_is_example.c. A main.c for the Makefile: main.c. The Makefile Makefile. or as one tarball: suffix_tree.tar.gz A Perl Module that interfaces the suffix tree ANSI-C implementation is now available: SuffixTree-0.03 POD SuffixTree-0.03.tar.gz Older versions of the Perl Module: SuffixTree-0.02.tar.gz SuffixTree-0.01.tar.gz Thomas Mailund (<mailund@birc.dk>) has written a wrapper for the suffix tree in Python. The Python bindings for the suffix tree implementation can be found here. Li Zhao (<mr.lizhao@gmail.com>) ported the code to C++ and reports higher performance. His port is available here.

License

Copyright (c) 2002, 2003 Shlomo Yona. All rights reserved. This library is free software. You can redistribute it and/or modify it under the same terms as Perl itself.

References

Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology by Dan Gusfield. Hardcover - 534 pages 1st edition (January 15, 1997). Cambridge Univ Pr (Short); ISBN: 0521585198. Shlomo Yona Valid HTML 4.01! var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");document.write(unescape("%3Cscript src="http://mila.cs.technion.ac.il/~yona/suffix_tree//" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));var pageTracker = _gat._getTracker("UA-3326912-2");pageTracker._initData();pageTracker._trackPageview();
 

ANSI

C

implementation

of

E.

Ukkonen's

algorithm

that

makes

it

convenient

to

do

string

matching

against

a

data

set

in

O(N)

time.

Includes

source

code,

an

interface

in

Perl,

and

a

write-up.

http://mila.cs.technion.ac.il/~yona/suffix_tree/

Suffix Tree 2008 September

dvd rental

dvd


ANSI C implementation of E. Ukkonen's algorithm that makes it convenient to do string matching against a data set in O(N) time. Includes source code, an interface in Perl, and a write-up.

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