Struct OrphosConfig 

pub struct OrphosConfig {
    pub metagenomic: bool,
    pub closed_ends: bool,
    pub circular: 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. This does not enable wraparound gene detection; use circular for that.

Default: false (allow edge genes)

circular: bool

Treat sequences as circular topology for wraparound gene detection.

When true, sequence end and start are treated as adjacent so genes can span the breakpoint. This is independent from closed_ends.

Default: false (linear topology)

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.