Struct light_phylogeny::Options

source ·

pub struct Options {Show 32 fields
    pub branch: bool,
    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 tidy: bool,
    pub tidy_leaves_check: 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,
    pub gthickness: usize,
    pub sthickness: usize,
    pub squaresize: f32,
    pub trans_start: Option<String>,
    pub trans_end: Option<String>,
    pub mid_dist: bool,
}

Expand description

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§

§branch: bool

Display branch length

§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).

§tidy: bool

Tidy option

§tidy_leaves_check: bool

Tidy option

§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.

§gthickness: usize

thickness of the stroke for gene trees

§sthickness: usize

thickness of the stroke for species trees

§squaresize: f32

used for the size of square, circle, etc.

§trans_start: Option<String>

start transfert

§trans_end: Option<String>

end transfert

§mid_dist: bool

place les duplication et les branchingout a mi distance de leur parent

Implementations§

source §

impl Options

source

pub fn new() -> Self

Examples found in repository ?

examples/read_phyloxml_bug.rs (line 5)

fn main() {
    let mut tree: ArenaTree<String> = ArenaTree::default();
    let options: Options = Options::new();
    let config: Config = Config::new();
    read_phyloxml("examples/newick.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml.svg".to_string());
    println!("Please open output file 'read_phyloxml.svg' with your browser");
}

More examples

Hide additional examples

examples/read_newick_bug.rs (line 5)

fn main() {
    let mut tree: ArenaTree<String> = ArenaTree::default();
    let options: Options = Options::new();
    let config: Config = Config::new();
    read_newick("examples/rec0.recphyloxml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_clado.svg".to_string());
    println!("Please open output file 'read_newick_clado.svg' with your browser");

}

examples/read_recphyloxml_bug.rs (line 8)

fn main() {

    let transfers = vec![];
    let mut options: Options = Options::new();
    options.free_living = true;

    let config: Config = Config::new();
    // Version portrait
    let mut sp_tree: ArenaTree<String> = ArenaTree::default();
    let mut gene_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
    let mut global_roots: std::vec::Vec<usize> = Vec::new();
    read_recphyloxml_multi("examples/file_bug.recphylo".to_string(),
        &mut sp_tree, &mut gene_trees, &mut global_roots);
    recphyloxml_processing(&mut sp_tree, &mut gene_trees, &mut options, &config, true,
         &transfers, "read_recphyloxml_portrait.svg".to_string());
    println!("Please open output file 'read_recphyloxml_portrait.svg' with your browser");


}

examples/read_recphyloxml_prune.rs (line 8)

fn main() {

    let transfers = vec![];
    let mut options: Options = Options::new();
    let config: Config = Config::new();
    // Version portrait
    options.species_internal = true;
    let mut sp_tree: ArenaTree<String> = ArenaTree::default();
    let mut gene_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
    let mut global_roots: std::vec::Vec<usize> = Vec::new();
    read_recphyloxml_multi("examples/gene_parasite_page4.recphylo".to_string(),
        &mut sp_tree, &mut gene_trees, &mut global_roots);
    recphyloxml_processing(&mut sp_tree, &mut gene_trees, &mut options, &config, true,
         &transfers, "read_recphyloxml_portrait.svg".to_string());
    println!("Please open output file 'read_recphyloxml_portrait.svg' with your browser");




}

examples/read_recphyloxml_specloss.rs (line 11)

fn main() {

    // ============================================================================================
    // Version portrait
    let transfers = vec![];
    let mut options: Options = Options::new();
    let config: Config = Config::new();
    let mut sp_tree: ArenaTree<String> = ArenaTree::default();
    let mut gene_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
    let mut global_roots: std::vec::Vec<usize> = Vec::new();
    read_recphyloxml_multi("examples/example_obsolete_specloss.xml".to_string(),
        &mut sp_tree, &mut gene_trees, &mut global_roots);
    recphyloxml_processing(&mut sp_tree, &mut gene_trees, &mut options, &config, true,
         &transfers, "example_obsolete_specloss.svg".to_string());
    println!("Please open output file 'example_obsolete_specloss.svg' with your browser");

}

examples/read_recphyloxml_free_living.rs (line 8)

fn main() {

    let transfers = vec![];
    let mut options: Options = Options::new();
    let config: Config = Config::new();

    options.free_living = true;
    options.gene_internal = true;
    options.species_internal = true;


    let mut sp_tree: ArenaTree<String> = ArenaTree::default();
    let mut gene_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
    let mut global_roots: std::vec::Vec<usize> = Vec::new();
    read_recphyloxml_multi("examples/free_living_reconciliated.recphylo".to_string(),
        &mut sp_tree, &mut gene_trees, &mut global_roots);
    recphyloxml_processing(&mut sp_tree, &mut gene_trees, &mut options, &config, true,
         &transfers, "read_recphyloxml_free_living_reconciliated.svg".to_string());
    println!("Please open output file 'read_recphyloxml_free_living_reconciliated.svg' with your browser");

}