Function light_phylogeny::phyloxml_processing

source · 
pub fn phyloxml_processing(
    tree: &mut ArenaTree<String>,
    options: &Options,
    config: &Config,
    outfile: String
)
Expand description

Create a svg of the tree in phyloxml context.

Examples found in repository?
examples/read_phyloxml_bug.rs (line 8)
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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_newick_bug.rs (line 8)
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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");

}
examples/lca.rs (line 28)
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fn main() {
    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    let config: Config = Config::new();
    println!("Reading newick file examples/newick.A4.txt...");
    let contents = fs::read_to_string("examples/newick.A4.txt")
                .expect("Something went wrong reading the newick file");
                println!("Create a first node which will be the root...");
                let root = tree.new_node("Root".to_string());
                println!("Build the tree from the file contents...");
                newick2tree(contents, &mut tree, root, &mut 0);
                let j = tree.get_index("J".to_string()).expect("Error : unable to find J");
                println!("Index of leaf J is {}",j);
                let l = tree.get_index("L".to_string()).expect("Error : unable to find L");
                println!("Index of leaf L is {}",l);
                let n = tree.get_index("N".to_string()).expect("Error : unable to find N");
                println!("Index of leaf N is {}",n);
                let lca_jl = lca(&mut tree,j,l);
                println!("Index of lca betwen J and L is {}",lca_jl);
                tree.arena[lca_jl].name = "LCA of J and L".to_string();
                let lca_jn = lca(&mut tree,j,n);
                println!("Index of lca betwen J and N is {}",lca_jn);
                tree.arena[lca_jn].name = "LCA of J and N".to_string();
                // Display internal nodes
                options.gene_internal = true ;
                phyloxml_processing(&mut tree, &options, &config,"lca.svg".to_string());

                println!("Please open output file 'lca.svg' with your browser");
                println!("OK.");
}
examples/read_phyloxml_stroke_thickness.rs (line 10)
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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/build_tree.rs (line 56)
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fn main() {
    let mut tree: ArenaTree<String> = ArenaTree::default();
    let mut options: Options = Options::new();
    let config: Config = Config::new();

    // Create a new node root
    let root = tree.new_node("root".to_string());
    // Create  new nodes
    let a1 = tree.new_node("a1".to_string());
    let a2 = tree.new_node("a2".to_string());
    let a = tree.new_node("a".to_string());
    let b = tree.new_node("b".to_string());
    let c = tree.new_node("c".to_string());
    let d = tree.new_node("d".to_string());
    println!("Initial tree :");
    summary(&mut tree);

    // Set names
    tree.arena[root].name = "MyRoot".to_string();
    tree.arena[a].name = "Gene A".to_string();
    tree.arena[a1].name = "Gene A1".to_string();
    tree.arena[a2].name = "Gene A2".to_string();
    tree.arena[b].name = "Gene B".to_string();
    tree.arena[c].name = "Gene C".to_string();
    tree.arena[d].name = "Gene D".to_string();
    println!("");
    println!("Tree after name attribution:");
    summary(&mut tree);
    // Set hierarchy
    //  a1 and a2 are children of a
    tree.arena[a1].parent = Some(a);
    tree.arena[a2].parent = Some(a);
    tree.arena[a].children.push(a1);
    tree.arena[a].children.push(a2);
    // a and b are children of c
    tree.arena[a].parent = Some(c);
    tree.arena[b].parent = Some(c);
    tree.arena[c].children.push(a);
    tree.arena[c].children.push(b);
    // c and d are children of root
    tree.arena[c].parent = Some(root);
    tree.arena[d].parent = Some(root);
    tree.arena[root].children.push(c);
    tree.arena[root].children.push(d);
    println!("");
    println!("Tree after hierarchy attribution:");
    summary(&mut tree);

    // set duplication
    tree.arena[a].e = Event::Duplication;
    println!("");
    println!("Event associated to gene {} ({}) : {:?}",a,tree.arena[a].name,tree.arena[a].e);
    // Display internal nodes
    options.gene_internal = true ;
    phyloxml_processing(&mut tree, &options, &config,"build_tree.svg".to_string());
    println!("Please open output file 'build_tree.svg' with your browser");
    println!("OK.");
}
examples/read_phyloxml_tidy.rs (line 15)
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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");

}
Additional examples can be found in: