Function light_phylogeny::read_newick

source · 
pub fn read_newick(filename: String, tree: &mut ArenaTree<String>)
Expand description

Read a newick file and store the tree into ArenaTree structure.

Examples found in repository?
examples/read_newick_bug.rs (line 7)
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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");

}
More examples
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examples/read_phyloxml_tidy_virus.rs (line 13)
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fn main() {
    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 4.0;
    options.rotate = false;
    // options.support = true;
    // options.gene_internal = true;
    options.branch = true;
    let config: Config = Config::new();
    read_newick("examples/virus.nhx".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real_virus.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_real_virus.svg' with your browser");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 4.0;
    options.rotate = false;
    options.tidy = true;
    // options.support = true;
    // options.gene_internal = true;
    options.branch = true;
    let config: Config = Config::new();
    read_newick("examples/virus.nhx".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real_virus_tidy.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_real_virus_tidy.svg' with your browser");



    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 4.0;
    // options.rotate = false;
    options.tidy = true;
    options.tidy_leaves_check = true;
    // options.support = true;
    // options.gene_internal = true;
    options.branch = true;
    let config: Config = Config::new();
    read_newick("examples/virus.nhx".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real_virus_portrait_tidy_check.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_real_virus_portrait_tidy_check.svg' with your browser");


    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 4.0;
    // options.rotate = false;
    options.tidy = true;
    options.tidy_leaves_check = true;
    // options.support = true;
    // options.gene_internal = true;
    // options.branch = true;
    let mut config: Config = Config::new();
    config.gene_police_size = "50.0".to_string();
    read_newick("examples/virus.nhx".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real_virus_portrait_tidy_check_police.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_real_virus_portrait_tidy_check_police.svg' with your browser");


    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 4.0;
    // options.rotate = false;
    options.tidy = true;
    // options.tidy_leaves_check = true;
    // options.support = true;
    // options.gene_internal = true;
    // options.branch = true;
    let mut config: Config = Config::new();
    config.gene_police_size = "50.0".to_string();
    read_newick("examples/virus.nhx".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real_virus_portrait_tidy_police.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_real_virus_portrait_tidy_police.svg' with your browser");




    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 4.0;
    // options.rotate = false;
    // options.support = true;
    // options.gene_internal = true;
    options.branch = true;
    let config: Config = Config::new();
    read_newick("examples/virus.nhx".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real_virus_portrait.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_real_virus_portrait.svg' with your browser");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 4.0;
    // options.rotate = false;
    options.tidy = true;
    // options.support = true;
    // options.gene_internal = true;
    options.branch = true;
    let config: Config = Config::new();
    read_newick("examples/virus.nhx".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real_virus_portrait_tidy.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_real_virus_portrait_tidy.svg' with your browser");

}
examples/read_newick.rs (line 7)
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fn main() {
    let mut tree: ArenaTree<String> = ArenaTree::default();
    let options: Options = Options::new();
    let config: Config = Config::new();
    read_newick("examples/newick.txt".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");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.rotate = false;
    let mut config: Config = Config::new();
    config.gene_police_size = "50.0".to_string();
    read_newick("examples/newick.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_real_landcsape.svg".to_string());
    println!("Please open output file 'read_newick_real_landcsape.svg' with your browser");


    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    let mut config: Config = Config::new();
    config.gene_police_size = "50.0".to_string();
    read_newick("examples/newick.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_real_portrait.svg".to_string());
    println!("Please open output file 'read_newick_real_portrait.svg' with your browser");


    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.rotate = false;
    options.scale = 5.0;
    options.branch = true;
    options.tidy = true;
    let config: Config = Config::new();
    read_newick("examples/newick.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_real_by5_tidy_landcsape.svg".to_string());
    println!("Please open output file 'read_newick_real_by5_tidy_landcsape.svg' with your browser");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    // options.rotate = false;
    options.scale = 4.0;
    options.branch = true;
    options.tidy = true;
    let mut config: Config = Config::new();
    config.gene_police_size = "50.0".to_string();
    read_newick("examples/newick.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_real_by4_tidy.svg".to_string());
    println!("Please open output file 'read_newick_real_by4_tidy.svg' with your browser");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.rotate = false;
    options.scale = 5.0;
    options.branch = true;
    let config: Config = Config::new();
    read_newick("examples/newick.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_real_by5_landcsape.svg".to_string());
    println!("Please open output file 'read_newick_real_by5_landcsape.svg' with your browser");


    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.rotate = false;
    let config: Config = Config::new();
    read_newick("examples/newick.220.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_220_real_landscape.svg".to_string());
    println!("Please open output file 'read_newick_220_real_landscape.svg' with your browser");



    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 5.0;
    options.support = true;
    let config: Config = Config::new();
    read_newick("examples/newick.220.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_220_real_by5_support.svg".to_string());
    println!("Please open output file 'read_newick_220_real_by5_support.svg' with your browser");


    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 5.0;
    let config: Config = Config::new();
    read_newick("examples/newick.220.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_220_real_by5.svg".to_string());
    println!("Please open output file 'read_newick_220_real_by5.svg' with your browser");



    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.rotate = false;
    let config: Config = Config::new();
    read_newick("examples/newick.220.txt".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_newick_220_landscape.svg".to_string());
    println!("Please open output file 'read_newick_220_landscape.svg' with your browser");


}