Struct SeqIdHit 

pub struct SeqIdHit {

    pub accession: String,
    pub description: String,
    pub identity: f32,
    pub is_reverse: bool,
    pub kansasii_gastri_snp_calls: Vec<KansasiiGastriSnpCall>,
    pub marinum_ulcerans_snp_calls: Vec<MarinumUlceransSnpCall>,
    pub rrl_snp_calls: Vec<RrlSnpCall>,
    pub rrs_snp_calls: Vec<RrsSnpCall>,
    pub erm41_snp_calls: Vec<Erm41LofCall>,
    pub pnca_snp_calls: Vec<PncaSnpCall>,
    pub aligned_query: Vec<u8>,
    pub aligned_ref: Vec<u8>,
    pub ref_start: usize,
    pub erm41_position_28_opt: Option<Erm41Position28>,
    pub rrl_position_2058_2059_opt: Option<RrlPosition2058_2059>,
}

Best-hit result from aligning an AB1 read against the reference sequences.

Fields

accession: String

Accession of the best-matching reference (e.g. “AF547836”).

description: String

Species name stripped to genus + species (e.g. “Mycobacterium gastri”).

identity: f32

Percent identity of the best local alignment window (0.0–100.0).

is_reverse: bool

true when the reverse complement of the query was the better match.

kansasii_gastri_snp_calls: Vec<KansasiiGastriSnpCall>

Calls at each diagnostic kansasii/gastri SNP position.

marinum_ulcerans_snp_calls: Vec<MarinumUlceransSnpCall>

Calls at each diagnostic marinum/ulcerans SNP position.

rrl_snp_calls: Vec<RrlSnpCall>

Calls at each rrl macrolide-resistance SNP position (23S rRNA).

rrs_snp_calls: Vec<RrsSnpCall>

Calls at each rrs aminoglycoside-resistance SNP position (16S rRNA).

erm41_snp_calls: Vec<Erm41LofCall>

Calls at each erm(41) loss-of-function variant position.

pnca_snp_calls: Vec<PncaSnpCall>

Calls at each pncA pyrazinamide-resistance nucleotide/codon position.

aligned_query: Vec<u8>

Gapped query sequence (forward or RC, whichever scored best). '-' marks deletions.

aligned_ref: Vec<u8>

Gapped reference sequence for the aligned span. Same length as aligned_query.

ref_start: usize

0-based position in the full reference where the alignment starts.

erm41_position_28_opt: Option<Erm41Position28>

Erm41 position 28 call; None for non-erm41 targets.

rrl_position_2058_2059_opt: Option<RrlPosition2058_2059>

rrl position 2058 2059 call; None for non-rrl targets.

Implementations

impl SeqIdHit

pub fn format_pairwise_alignment(&self) -> String

Format the alignment as a human-readable pairwise text (60-column wrapping).

pub fn is_kansasii(&self) -> bool

pub fn is_gastri(&self) -> bool

pub fn is_marinum(&self) -> bool

pub fn is_ulcerans(&self) -> bool

pub fn kansasii_gastri_snp_species_call(&self) -> Option<&'static str>

pub fn marinum_ulcerans_snp_species_call(&self) -> Option<&'static str>

Trait Implementations

impl Clone for SeqIdHit

fn clone(&self) -> SeqIdHit

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for SeqIdHit

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for SeqIdHit

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for SeqIdHit

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.