Struct light_phylogeny::Options

pub struct Options {

    pub gene_internal: bool,
    pub species_internal: bool,
    pub clado_flag: bool,
    pub species_only_flag: bool,
    pub real_length_flag: bool,
    pub open_browser: bool,
    pub verbose: bool,
    pub disp_gene: usize,
    pub scale: f32,
    pub ratio: f32,
    pub rotate: bool,
    pub remove: bool,
    pub thickness_flag: bool,
    pub thickness_thresh: usize,
    pub thickness_gene: usize,
    pub thickness_disp_score: bool,
    pub optimisation: bool,
    pub height: f32,
    pub width: f32,
    pub support: bool,
    pub free_living: bool,
    pub free_living_shift: bool,
    pub uniform: bool,
}

Structure Options: these are the drawing options for the svg. Concerning recPhyloXML file, we assume in the documentation that it describes a gene/species reconciliation.

Fields

gene_internal: bool

Display internal gene nodes.

species_internal: bool

Display internal species nodes (recPhyloXML).

clado_flag: bool

Display a cladogramme.

species_only_flag: bool

Only draw the species tree (recPhyloXML).

real_length_flag: bool

Use the real branch length.

open_browser: bool

Open the svg in the browser.

verbose: bool

Verbose mode.

disp_gene: usize

Only draw gene tree number # (recPhyloXML).

scale: f32

Scale to be applied to real branch length.

ratio: f32

Ratio between species pipe tree width and cumulated gene trees width (recPhyloXML).

rotate: bool

Rotate the svg 90 counter clockwise.

remove: bool

Not yet implemented.

thickness_flag: bool

Draw only one transfer to represent redundant transfers (recPhyloXML).

thickness_thresh: usize

Abundance threshold for displaying redundant transfers (recPhyloXML).

thickness_gene: usize

Number of the gene tree to display when displaying redundant transfers as one (recPhyloXML).

thickness_disp_score: bool

Display the abundance of the redundant transfers (recPhyloXML).

optimisation: bool

Optimise species branches left/right orientation in order to minimise transfer crossings (recPhyloXML, under development).

height: f32

Scale to be applied to the heigth of the tree.

width: f32

Width to be applied to the heigth of the tree.

support: bool

Display support.

free_living: bool

Support “free living” species (i.e. not associated to a species of the species tree) in the gene tree(s).

free_living_shift: bool

With free_living option : in case of multriple gene trees, shifting free living trees instead superposing.

uniform: bool

Uniformise the species tree nodes size.

Implementations

impl Options

pub fn new() -> Self

Trait Implementations

impl Debug for Options

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

Formats the value using the given formatter.