Struct OrphosConfig 

pub struct OrphosConfig {
    pub metagenomic: bool,
    pub closed_ends: bool,
    pub mask_n_runs: bool,
    pub force_non_sd: bool,
    pub quiet: bool,
    pub output_format: OutputFormat,
    pub translation_table: Option<u8>,
    pub num_threads: Option<usize>,
}

Configuration settings for Orphos gene prediction analysis.

This struct controls all aspects of gene prediction including analysis mode, sequence handling, and output formatting.

Examples

Default configuration

use orphos_core::config::OrphosConfig;

let config = OrphosConfig::default();

Custom configuration for closed-ended genomes

use orphos_core::config::{OrphosConfig, OutputFormat};

let config = OrphosConfig {
    closed_ends: true,
    mask_n_runs: true,
    output_format: OutputFormat::Gff,
    ..Default::default()
};

Metagenomic mode with multiple threads

use orphos_core::config::OrphosConfig;

let config = OrphosConfig {
    metagenomic: true,
    num_threads: Some(8),
    quiet: true,
    ..Default::default()
};

Fields

metagenomic: bool

Enable metagenomic mode for fragmented sequences.

When true, uses pre-computed models instead of training on each sequence. Recommended for:

• Short contigs (< 100 kb)
• Mixed community samples
• Fragmented assemblies

Default: false (single genome mode)

closed_ends: bool

Treat sequences as having closed ends (complete genomes).

When true, prevents genes from extending off sequence edges. Use for complete, circularized genomes.

Default: false (allow edge genes)

mask_n_runs: bool

Mask runs of N characters during analysis.

When true, treats stretches of N’s as gaps and prevents genes from spanning them. Useful for draft genomes with gaps.

Default: false

force_non_sd: bool

Force use of non-Shine-Dalgarno models for start recognition.

When true, disables detection of ribosome binding sites. Rarely needed except for organisms without canonical RBS.

Default: false (auto-detect)

quiet: bool

Suppress informational output during processing.

When true, prevents progress messages and statistics from being printed to stderr.

Default: false

output_format: OutputFormat

Output format for gene prediction results.

Controls the format of generated output files. See OutputFormat for available options.

Default: OutputFormat::Genbank

translation_table: Option<u8>

Genetic code translation table number (1-25).

Specifies which genetic code to use for translation:

• 11: Bacterial/Archaeal (most common, default)
• 4: Mycoplasma/Spiroplasma
• Others: See NCBI genetic code tables

Default: None (auto-detect, usually table 11)

num_threads: Option<usize>

Number of threads to use for parallel processing.

When set, configures Rayon thread pool for parallel analysis of multiple sequences. Set to None for automatic detection.

Default: None (use all available cores)

Trait Implementations

impl Clone for OrphosConfig

fn clone(&self) -> OrphosConfig

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for OrphosConfig

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for OrphosConfig

fn default() -> Self

Returns the “default value” for a type.