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prex

Approximate Regular Expression Matching for Java. prex determines the matching distance between a string s and a regular expression r, i.e. how many insertions, deletions and substitutions on s are at least required (minimum cost) such that the resulting string s' is acceptable by r.

Status

License: MIT Language Linux Build Status Test Coverage Code Climate

Approach

The prex algorithm is inspired by the work of Myers and Millers who provide an algorithm for solving the approximate regular expression matching problem. However, their approach requires a special pre-computed data-structure called edit-graph e that encodes all possible matches and mismatches of s with respect to r which requires approximately 15xSxR edges and SxR vertices where S denotes the length of s and R is the length of r. Given that data structure, their approach searches a minimal cost path in e with a worst-case time complexity of O(SxR). The main strengths of Myers and Millers approach are the possibility to use real-valued costs for insertion, deletion and substitution, respectively, and its worst-case time complexity. The drawback, however, is that the edit-graph has to be created upfront.

Similar to Myers and Millers approach, one can also define real-valued cost for deletion, insertion and substitution in prex. However, prex is based on the branch and bounds method (+ extended list) and does not rely on a precomputed edit-graph. Because, prex is using branch and bounds, in theory it has the same worst-case time complexity as exhaustive search. However, our goal is to keep the algorithm as simple as possible and to achieve a reasonable performance in practice by incorporating heuristics.

Usage

prex can be used as a standalone command line tool or as a library.

Standalone

One could compile prex by running mvn package on the command line. The resulting jar archive can be called with java -jar prex.jar and provides the following command line options:

Option Description
-c,--cost <cost> cost values <insertion> <substitution> <deletion>
-h print this message
-ic,--ignore-case ignore case of s when matching against r
-n,--normalize normalize cost to a value in range [0,1]
-r,--regex <regex> regular expression
-s,--string <string> constant string
-t,--print-tree print branch and bounds edit tree

Please note that the regex syntax is based on dk.brics and that paramters passed to prex should be quoted to prevent globbing. In case you need quotes with inside your string or you regex pattern, you could escape them as illustrated in the example below.

java -jar prex.jar -c 1.0 1.0 1.0 -s "\"" -r "\\\""
input-string: '"'
input-regex: '\"'
Cost : 0.0

The pattern \" for the s parameter is equivalent to the quote character since it is treated as a normal Java string. The parameter passed through the r paramter is interpreted differently, because the regular expression syntax is based on dk.brics; the pattern \\\" is interpreted as a quote charater.

Library

The following code snippet shows how to use prex after the jar file is imported into your project:

// invoke Prex constructor with regular expression definition,
// r = gcg[abc]+
// default costs for substitution, insertion and deletion are 1.0,
// but they are modifiable
Prex am = new Prex("gcg[abc]+");
// get cost to make s = GCGa matching r = gcg[abc]+
// ignore case and return a value in range [0,1]
System.out.println(am.evaluateCost("GCGa", true, true));
// get cost to make s = GCGa matching r = gcg[abc]+
// do not ignore case and return a value in range [0,1]
System.out.println("GCGa", false, true));
// ignore case and do not normalize
System.out.println(am.evaluateCost("GCGa", true, false));
// do not ignore case and do not normalize
System.out.println(am.evaluateCost("GCGa", false, false));

The results of the invocations above look as follows:

0.0
0.75
0.0
3.0

Please have a look at the test cases and constructors provided by the Prex Java class to get additional information about the usage of prex.

Licence

The MIT License (MIT)

Copyright (c) 2016 Julian Thome [email protected]

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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