Aho-Corasick is an optimal algorithm for finding many keywords in a text. It can locate all matches in a text in O(N+M) time; i.e., the time needed scales linearly with the number of keywords (N) and the size of the text (M). Compare this to the naive approach which takes O(N*M) time to loop through each pattern and scan for it in the text. This implementation builds the trie (the generic name of the data structure) and runs the search in a single function call. If you want to search multiple texts with the same trie, the function will take a list or vector of texts and return a list of matches to each text. By default, all 128 ASCII characters are allowed in both the keywords and the text. A more efficient trie is possible if the alphabet size can be reduced. For example, DNA sequences use at most 19 distinct characters and usually only 4; protein sequences use at most 26 distinct characters and usually only 20. UTF-8 (Unicode) matching is not currently supported.
Version: | 0.1.0 |
Imports: | Rcpp (≥ 0.12.5) |
LinkingTo: | Rcpp |
Suggests: | Biostrings, microbenchmark |
Published: | 2016-07-29 |
Author: | Matt Chambers [aut, cre], Tomas Petricek [aut, cph], Vanderbilt University [cph] |
Maintainer: | Matt Chambers <matt.chambers42 at gmail.com> |
BugReports: | https://github.com/chambm/AhoCorasickTrie/issues |
License: | Apache License 2.0 |
URL: | https://github.com/chambm/AhoCorasickTrie |
NeedsCompilation: | yes |
SystemRequirements: | C++11 |
CRAN checks: | AhoCorasickTrie results |
Reference manual: | AhoCorasickTrie.pdf |
Package source: | AhoCorasickTrie_0.1.0.tar.gz |
Windows binaries: | r-devel: AhoCorasickTrie_0.1.0.zip, r-release: AhoCorasickTrie_0.1.0.zip, r-oldrel: AhoCorasickTrie_0.1.0.zip |
OS X Mavericks binaries: | r-release: AhoCorasickTrie_0.1.0.tgz, r-oldrel: AhoCorasickTrie_0.1.0.tgz |
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