Struct goat_cli::utils::url::FieldBuilder

pub struct FieldBuilder {

    pub taxon_assembly: bool,
    pub taxon_bioproject: bool,
    pub taxon_busco: bool,
    pub taxon_country_list: bool,
    pub taxon_cvalues: bool,
    pub taxon_date: bool,
    pub taxon_gc_percent: bool,
    pub taxon_gene_count: bool,
    pub taxon_gs: bool,
    pub taxon_karyotype: bool,
    pub taxon_legislation: bool,
    pub taxon_mitochondrion: bool,
    pub taxon_n50: bool,
    pub taxon_names: bool,
    pub taxon_plastid: bool,
    pub taxon_ploidy: bool,
    pub taxon_sex_determination: bool,
    pub taxon_status: bool,
    pub taxon_target_lists: bool,
    pub taxon_tidy: bool,
    pub assembly_assembly: bool,
    pub assembly_karyotype: bool,
    pub assembly_contig: bool,
    pub assembly_scaffold: bool,
    pub assembly_gc: bool,
    pub assembly_gene: bool,
    pub assembly_busco: bool,
    pub assembly_btk: bool,
}

Boolean struct containing all of the CLI flag information passed from the user. This struct has been expanded to include both taxon and assembly indexes.

Fields

taxon_assembly: bool

Add only assembly level/span GoaT fields.

A taxon index flag.

taxon_bioproject: bool

Add bioproject GoaT field.

A taxon index flag.

taxon_busco: bool

Add BUSCO completeness.

A taxon index flag.

taxon_country_list: bool

Add country list GoaT field.

A taxon index flag.

taxon_cvalues: bool

Add C-value information GoaT field.

A taxon index flag.

taxon_date: bool

Add assembly & EBP metric date GoaT fields.

A taxon index flag.

taxon_gc_percent: bool

Add GC percent GoaT field.

A taxon index flag.

taxon_gene_count: bool

Add gene count GoaT field.

A taxon index flag.

taxon_gs: bool

Add genome size GoaT fields.

A taxon index flag.

taxon_karyotype: bool

Add karyotype GoaT fields; chromosome number and haploid number.

A taxon index flag.

taxon_legislation: bool

Add return information for isb_wildlife_act_1976, habreg_2017, marhabreg-2017, waca_1981, protection_of_badgers_act_1992, echabs92

A taxon index flag.

taxon_mitochondrion: bool

Add mitochondrial assembly span and gc percent GoaT fields.

A taxon index flag.

taxon_n50: bool

Add contig and scaffold n50 GoaT fields.

A taxon index flag.

taxon_names: bool

Add synonym, tolID, and common name GoaT fields.

Not implemented in FieldBuilder below.

A taxon index flag.

taxon_plastid: bool

Add plastid assembly span and gc percent GoaT fields.

A taxon index flag.

taxon_ploidy: bool

Add ploidy GoaT field.

A taxon index flag.

taxon_sex_determination: bool

Add sex determination GoaT field.

A taxon index flag.

taxon_status: bool

Add sample tracking information GoaT field.

A taxon index flag.

taxon_target_lists: bool

Add long_list, other_priority, and family_representative GoaT fields.

A taxon index flag.

taxon_tidy: bool

Render output in tidy format?

Not implemented in FieldBuilder below.

A taxon index flag.

assembly_assembly: bool

Assembly span and level.

An assembly index flag.

assembly_karyotype: bool

Only chromosome count.

An assembly index flag.

assembly_contig: bool

All the contig information.

An assembly index flag.

assembly_scaffold: bool

All scaffold information.

An assembly index flag.

assembly_gc: bool

GC content.

An assembly index flag.

assembly_gene: bool

Gene and non-coding gene count.

An assembly index flag.

assembly_busco: bool

BUSCO completeness, lineage and string.

An assembly index flag.

assembly_btk: bool

BlobToolKit stats(?). No hit/target.

An assembly index flag.

Implementations

impl FieldBuilder

fn to_vec_tuples(&self) -> Vec<(bool, Vec<&str>)>

A function to turn all of the fields into a small data structure.

This is hardcoded, but could be modified to be read in from the goat standard variables JSON in the future.

It’s a Vec of a tuple of:

• bool which shows whether the user chose this flag or not
• Vec<&str> which enumerates the variable strings (as GoaT would recognise) that correspond to this field.

It’s a bit of a judgement call on my part but happy to change if there is a compelling argument.

pub fn build_fields_string(&self) -> String

A function which formats all of the GoaT fields together into a URL segment.

fn generate_exculde_flags(&self) -> String

An implementation of exculding values returned if they are missing or ancestral values inferred by GoaT.

Trait Implementations

impl Clone for FieldBuilder

fn clone(&self) -> FieldBuilder

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Copy for FieldBuilder