Function light_phylogeny::read_phyloxml

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

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

Examples found in repository?
examples/read_phyloxml_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_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
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examples/read_phyloxml_stroke_thickness.rs (line 9)
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fn main() {

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.rotate = false;
    let config: Config = Config::new();
    read_phyloxml("examples/FAM036542_gene.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_stroke_thickness_1.svg".to_string());
    println!("Please open output file 'read_phyloxml_stroke_thickness_1.svg' with your browser");


    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.rotate = false;
    options.gthickness = 1;
    let config: Config = Config::new();
    read_phyloxml("examples/FAM036542_gene.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_stroke_thickness_2.svg".to_string());
    println!("Please open output file 'read_phyloxml_stroke_thickness_2.svg' with your browser");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.rotate = false;
    options.gthickness = 6;
    let config: Config = Config::new();
    read_phyloxml("examples/FAM036542_gene.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_stroke_thickness_3.svg".to_string());
    println!("Please open output file 'read_phyloxml_stroke_thickness_3.svg' with your browser");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.rotate = false;
    options.gthickness = 2;
    options.squaresize = 15.0;
    let config: Config = Config::new();
    read_phyloxml("examples/FAM036542_gene.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_stroke_thickness_4.svg".to_string());
    println!("Please open output file 'read_phyloxml_stroke_thickness_4.svg' with your browser");


}
examples/read_phyloxml_tidy.rs (line 14)
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fn main() {
    // landscape
    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 4.0;
    options.support = true;
    options.gene_internal = true;
    options.rotate = false;
    // options.branch = true;
    let config: Config = Config::new();
    read_phyloxml("examples/apaf_name.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_real.svg' with your browser");

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


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

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

}
examples/read_phyloxml.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_phyloxml("examples/FAM036542_gene.xml".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");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.rotate = false;
    options.gene_internal = true;
    let config: Config = Config::new();
    read_phyloxml("examples/FAM036542_gene.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_landscape.svg".to_string());
    println!("Please open output file 'read_phyloxml_landscape.svg' with your browser");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let options: Options = Options::new();
    let config: Config = Config::new();
    read_phyloxml("examples/apaf.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist.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.support = true;
    options.branch = true;
    options.gene_internal = true;
    let config: Config = Config::new();
    read_phyloxml("examples/apaf.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_real.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.support = true;
    options.branch = true;
    options.rotate = false;
    let config: Config = Config::new();
    read_phyloxml("examples/apaf.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_dist_real_landscape.svg".to_string());
    println!("Please open output file 'read_phyloxml_dist_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 = 4.0;
    options.support = true;
    let config: Config = Config::new();
    read_phyloxml("examples/bcl_2.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_events.svg".to_string());
    println!("Please open output file 'read_phyloxml_events.svg' with your browser");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 10.0;
    options.support = true;
    let config: Config = Config::new();
    read_phyloxml("examples/ENSGT00390000003602.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_ensembl.svg".to_string());
    println!("Please open output file 'read_phyloxml_ensembl.svg' with your browser");



    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 10.0;
    options.support = true;
    options.gene_colors.push("green".to_string());
    options.gene_colors.push("red".to_string());
    let config: Config = Config::new();
    read_phyloxml("examples/ENSGT00390000003602.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_ensembl_color.svg".to_string());
    println!("Please open output file 'read_phyloxml_ensembl_color.svg' with your browser");

    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.real_length_flag = true;
    options.scale = 10.0;
    options.support = true;
    options.gene_colors.push("green".to_string());
    options.gene_colors.push("red".to_string());
    options.node_colors.push("ENSTRUG00000006177".to_string());
    let config: Config = Config::new();
    read_phyloxml("examples/ENSGT00390000003602.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_ensembl_color_2.svg".to_string());
    println!("Please open output file 'read_phyloxml_ensembl_color_2.svg' with your browser");


    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.node_colors.push("02_speciation".to_string());
    options.node_colors.push("01_speciation".to_string());
    options.node_colors.push("b1".to_string());
    options.node_colors.push("b2".to_string());
    options.gene_internal = true;
    options.squaresize = 15.0;
    let config: Config = Config::new();
    read_phyloxml("xml_examples/example_dupli.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_example_dupli_color.svg".to_string());
    println!("Please open output file 'read_phyloxml_example_dupli_color.svg' with your browser");



    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    options.gene_colors.push("green".to_string());
    options.gene_colors.push("red".to_string());
    options.gene_colors.push("orange".to_string());
    options.node_colors.push("02_speciation".to_string());
    options.node_colors.push("01_speciation".to_string());
    options.node_colors.push("b1".to_string());
    options.node_colors.push("b2".to_string());
    options.gene_internal = true;
    options.squaresize = 15.0;
    let config: Config = Config::new();
    read_phyloxml("xml_examples/example_dupli.xml".to_string(), &mut tree);
    phyloxml_processing(&mut tree, &options, &config,"read_phyloxml_example_dupli_color_2.svg".to_string());
    println!("Please open output file 'read_phyloxml_example_dupli_color_2.svg' with your browser");



}