https://github.com/ajalab/fm-index
FM-Index for Rust
https://github.com/ajalab/fm-index
fm-index rust succinct-data-structure
Last synced: 3 months ago
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FM-Index for Rust
- Host: GitHub
- URL: https://github.com/ajalab/fm-index
- Owner: ajalab
- License: apache-2.0
- Created: 2019-10-07T14:28:56.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2025-02-23T06:05:08.000Z (3 months ago)
- Last Synced: 2025-02-23T07:17:55.686Z (3 months ago)
- Topics: fm-index, rust, succinct-data-structure
- Language: Rust
- Homepage:
- Size: 318 KB
- Stars: 9
- Watchers: 2
- Forks: 2
- Open Issues: 21
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES.md
- License: LICENSE-APACHE
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README
# fm-index
[](https://crates.io/crates/fm-index)
[](https://docs.rs/fm-index)
This crate provides implementations of
[FM-Index](https://en.wikipedia.org/wiki/FM-index) and its variants.
FM-Index, originally proposed by Paolo Ferragina and Giovanni Manzini [^1],
is a compressed full-text index which supports the following queries:
- `count`: Given a pattern string, counts the number of its occurrences.
- `locate`: Given a pattern string, lists the all positions of its occurrences.
- `extract`: Given an integer, gets the character of the text at that position.
The `fm-index` crate does not support the third query (extracting a
character from arbitrary position). Instead, it provides backward/forward
iterators that return the text characters starting from a search result.
## Usage
Add this to your `Cargo.toml`.
```toml
[dependencies]
fm-index = "0.2"
```
## Example
```rust
use fm_index::converter::RangeConverter;
use fm_index::FMIndex;
// Prepare a text string to search for patterns.
let text = concat!(
"Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.",
"Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.",
"Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.",
"Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.",
).as_bytes().to_vec();
// Converter converts each character into packed representation.
// `' '` ~ `'~'` represents a range of ASCII printable characters.
let converter = RangeConverter::new(b' ', b'~');
let index = SearchIndexBuilder::with_converter(converter)
// the sampling level determines how much is retained in order to support `locate`
// queries. `0` retains the full information, but we don't need the whole array
// since we can interpolate missing elements in a suffix array from others. A sampler
// will _sieve_ a suffix array for this purpose. If you don't need `locate` queries
// you can save the memory by not setting a sampling level.
.sampling_leveL(2)
.build(text);
// Search for a pattern string.
let pattern = "dolor";
let search = index.search_backward(pattern);
// Count the number of occurrences.
let n = search.count();
assert_eq!(n, 4);
// List the position of all occurrences.
let positions = search.locate();
assert_eq!(positions, vec![246, 12, 300, 103]);
// Extract preceding characters from a search position.
let i = 0;
let mut prefix = search.iter_backward(i).take(16).collect::>();
prefix.reverse();
assert_eq!(prefix, b"Duis aute irure ".to_owned());
// Extract succeeding characters from a search position.
let i = 3;
let postfix = search.iter_forward(i).take(20).collect::>();
assert_eq!(postfix, b"dolore magna aliqua.".to_owned());
// Search can be chained backward.
let search_chained = search.search_backward("et ");
assert_eq!(search_chained.count(), 1);
```
## Implementations
### FM-Index
The implementation is based on [^1].The index is constructed with a suffix
array generated by SA-IS [^3] in _O(n)_ time, where _n_ is the size of a text
string.
Basically it consists of
- a Burrows-Wheeler transform (BWT) of the text string represented with
_wavelet matrix_ [^4]
- an array of size _O(σ)_ (_σ_: number of characters) which stores the number
of characters smaller than a given character
- a (sampled) suffix array
### Run-Length FM-Index
Based on [^2]. The index is constructed with a suffix array generated by SA-IS
[^3].
It consists of
- a wavelet matrix that stores the run heads of BWT of the text string
- a succinct bit vector which stores the run lengths of BWT of the text string
- a succinct bit vector which stores the run lengths of BWT of the text string
sorted in alphabetical order of corresponding run heads
- an array of size _O(σ)_ (_σ_: number of characters) which stores the number
of characters smaller than a given character in run heads
## Reference
[^1]: Ferragina, P., & Manzini, G. (2000). Opportunistic data structures with
applications. Annual Symposium on Foundations of Computer Science \- Proceedings, 390–398.
[^2]: Mäkinen, V., & Navarro, G. (2005). Succinct suffix arrays based on
run-length encoding. In Lecture Notes in Computer Science (Vol. 3537).
[^3]: Ge Nong, Sen Zhang, & Wai Hong Chan. (2010). Two Efficient Algorithms for
Linear Time Suffix Array Construction. IEEE Transactions on Computers, 60(10),
1471–1484.
[^4]: Claude F., Navarro G. (2012). The Wavelet Matrix. In: Calderón-Benavides
L., González-Caro C., Chávez E., Ziviani N. (eds) String Processing and
Information Retrieval. SPIRE 2012.