Function light_phylogeny::read_recphyloxml_multi

source · 
pub fn read_recphyloxml_multi(
    filename: String,
    global_pipe: &mut ArenaTree<String>,
    gene_trees: &mut Vec<ArenaTree<String>>,
    global_roots: &mut Vec<usize>
)
Expand description

Read a recphyloxml file and store the species and gene trees into several ArenaTree structures.

Examples found in repository?
examples/read_recphyloxml_bug.rs (lines 16-17)
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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");


}
More examples
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examples/read_recphyloxml_prune.rs (lines 15-16)
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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 (lines 16-17)
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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 (lines 19-20)
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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");

}
examples/read_recphyloxml_free_living_2.rs (lines 19-20)
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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_2.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_2.svg".to_string());
    println!("Please open output file 'read_recphyloxml_free_living_reconciliated_2.svg' with your browser");

}
examples/read_recphyloxml_free_living_3.rs (lines 19-20)
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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_3.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_3.svg".to_string());
    println!("Please open output file 'read_recphyloxml_free_living_reconciliated_3.svg' with your browser");

}
Additional examples can be found in: