genomic_system_finder_core/lib.rs
1// SPDX-License-Identifier: GPL-3.0-or-later
2
3//! # genomic-system-finder-core
4//!
5//! Core library for Genomic System Finder — detection of macromolecular systems
6//! (secretion systems, CRISPR-Cas, pili, etc.) in protein sequences.
7//!
8//! ## Overview
9//!
10//! Genomic System Finder searches protein sequences against HMM profiles, clusters
11//! nearby hits, and evaluates candidate systems based on gene composition
12//! models. It supports:
13//!
14//! - **Ordered replicons**: assembled genomes with known gene order
15//! - **Unordered sequences**: draft/fragmented genomes
16//! - **Gembase format**: multi-replicon databases
17//!
18//! ## Architecture
19//!
20//! - [`config`]: Configuration and scoring parameters
21//! - [`model`]: System model definitions (mandatory, accessory, forbidden genes)
22//! - [`profile`]: HMM profile management and search
23//! - [`sequence`]: FASTA parsing and replicon handling
24//! - [`hit`]: HMM search hit representation
25//! - [`cluster`]: Gene clustering algorithms
26//! - [`system`]: System detection, scoring, and selection
27//! - [`report`]: Output generation (TSV, JSON)
28
29pub mod cluster;
30pub mod config;
31pub mod error;
32pub mod hit;
33pub mod model;
34pub mod profile;
35pub mod report;
36pub mod sequence;
37pub mod system;
38
39pub use config::{Config, ConfigBuilder, DbType, RepliconTopology};
40pub use error::MacsyError;
41pub use system::GenomicSystemFinder;