TRE (computing)

TRE
Original author(s)	Ville Laurikari
Repository	github.com/laurikari/tre ;
Written in	C
Type	Approximate string matching
License	2-clause BSD-like license
Website	laurikari.net/tre/

TRE is an open-source library for pattern matching in text,^[2] which works like a regular expression engine with the ability to do approximate string matching.^[3] It was developed by Ville Laurikari^[1] and is distributed under a 2-clause BSD-like license.

The library^[4] is written in C and provides functions which allow using regular expressions for searching over input text lines. The main difference from other regular expression engines is that TRE can match text fragments in an approximate way, that is, supposing that text could have some number of typos.

Features

TRE uses extended regular expression syntax with the addition of "directions" for matching preceding fragment in approximate way. Each of such directions specifies how many typos are allowed for this fragment.

Approximate matching^[5] is performed in a way similar to Levenshtein distance, which means that there are three types of typos 'recognized':^[6]

Typo	Example	Data
insertion of an extra character	regullar experession	extra l, extra e
missing a character from pattern	reglar expession	missing u, missing r
replacement of some character	regolar exprezsion	u → o, s → z

TRE allows specifying of cost for each of three typos type independently.

The project comes with a command-line utility, a reimplementation of agrep.

Though approximate matching requires some syntax extension, when this feature is not used, TRE works like most of other regular expression matching engines. This means that

it implements ordinary regular expressions written for strict matching;^[3]^[7]
programmers familiar with POSIX-style regular expressions^[4] need not do much study to be able to use TRE.^[3]

Predictable time and memory consumption

The library's author states^[8] that time spent for matching grows linearly with increasing of input text length, while memory requirement is constant during matching and does not depend on the input, only on the pattern.

Other

Other features, common for most regular expression engines could be checked in regex engines comparison tables or in list of TRE features on its web-page.

Usage example

Approximate matching directions are specified in curly brackets and should be distinguishable from repetitive quantifiers (possibly with inserting a space after opening bracket):

(regular){~1}\s+(expression){~2} would match variants of phrase "regular expression" in which "regular" have no more than one typo and "expression" no more than two; as in ordinary regular expressions "\s+" means one or more space characters - i.e. rogular ekspression would pass test;
(expression){ 5i + 3d + 2s < 11} would match word "expression" if total cost of typos is less than 11, while insertion cost is set to 5, deletion to 3 and substitution of character to 2 - i.e. ekspresson gives cost of 10.

Language bindings

Apart from C, TRE is usable through bindings for Perl, Python and Haskell. ^[9] It is the default regular expression engine in R.^[10] However if the project should be cross-platform, there would be necessary separate interface for each of the target platforms.

Disadvantages

Since other regular expression engines usually do not provide approximate matching ability, there is almost no concurrent implementation with which TRE could be compared. However there are a few things which programmers may wish to see implemented in future releases:^[11]

a replacement mechanism for substituting matched text fragments (like in sed string processor and many modern implementations of regular expressions, including built into Perl or Java);
opportunity to use another approximate matching algorithm (than Levenshtein's) for better typo value assessment (for example Soundex), or at least this algorithm to be improved to allow typos of the "swap" type (see Damerau–Levenshtein distance).

References

^ ^a ^b "R: Pattern Matching for Raw Vectors". MIT.edu.
^ "Tre for Windows".
^ ^a ^b ^c "Using fuzzy searches with tre-agrep". Linux Magazine.
^ ^a ^b "tre 0.8.0-6 (x86_64)". July 7, 2020.
^ Andoni, Alexandr; Krauthgamer, Robert; Onak, Krzysztof (2010). Polylogarithmic approximation for edit distance and the asymmetric query complexity. IEEE Symp. Foundations of Computer Science (FOCS). arXiv:1005.4033. Bibcode:2010arXiv1005.4033A. CiteSeerX 10.1.1.208.2079.
^ "TRE web-page - Regex Syntax".
^ "Tre-agrep has all of grep's functionality but can also do ambiguous or fuzzy"
^ "TRE web-page - About".
^ "TRE web-page - FAQ".
^ "Regular Expressions as used in R".
^ "Tagged Deterministic Finite Automata with Lookahead". practical improvements .. Lurikari algorithm, notably ..

External links

TRE - The free and portable approximate regular expression matching library

v t e Strings
String metric	Approximate string matching Bitap algorithm Damerau–Levenshtein distance Edit distance Gestalt pattern matching Hamming distance Jaro–Winkler distance Lee distance Levenshtein automaton Levenshtein distance Wagner–Fischer algorithm
String-searching algorithm	Apostolico–Giancarlo algorithm Boyer–Moore string-search algorithm Boyer–Moore–Horspool algorithm Knuth–Morris–Pratt algorithm Rabin–Karp algorithm Raita algorithm Trigram search Two-way string-matching algorithm Zhu–Takaoka string matching algorithm
Multiple string searching	Aho–Corasick Commentz-Walter algorithm
Regular expression	Comparison of regular-expression engines Regular grammar Thompson's construction Nondeterministic finite automaton
Sequence alignment	BLAST Hirschberg's algorithm Needleman–Wunsch algorithm Smith–Waterman algorithm
Data structure	DAFSA Suffix array Suffix automaton Suffix tree Generalized suffix tree Rope Ternary search tree Trie
Other	Parsing Pattern matching Compressed pattern matching Longest common subsequence Longest common substring Sequential pattern mining Sorting String rewriting systems String operations