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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: | 0.1.2 |
| Imports: | Rcpp (≥ 0.12.5) |
| LinkingTo: | Rcpp |
| Suggests: | Biostrings, microbenchmark, testthat |
| Published: | 2020-09-29 |
| DOI: | 10.32614/CRAN.package.AhoCorasickTrie |
| 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_0.1.2.tar.gz |
| Windows binaries: | r-devel: AhoCorasickTrie_0.1.2.zip, r-release: AhoCorasickTrie_0.1.2.zip, r-oldrel: AhoCorasickTrie_0.1.2.zip |
| macOS binaries: | r-release (arm64): AhoCorasickTrie_0.1.2.tgz, r-oldrel (arm64): AhoCorasickTrie_0.1.2.tgz, r-release (x86_64): AhoCorasickTrie_0.1.2.tgz, r-oldrel (x86_64): AhoCorasickTrie_0.1.2.tgz |
| Old sources: | AhoCorasickTrie archive |
| Reverse imports: | customProDB, prozor |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.