Function light_phylogeny::recphyloxml_processing
source · pub fn recphyloxml_processing(
sp_tree: &mut ArenaTree<String>,
gene_trees: &mut Vec<ArenaTree<String>>,
options: &mut Options,
config: &Config,
mapping: bool,
transfers: &Vec<(String, String)>,
outfile: String
)
Expand description
Create a svg of the tree in recphyloxml context.
Examples found in repository?
examples/read_recphyloxml_bug.rs (lines 18-19)
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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
examples/read_recphyloxml_prune.rs (lines 17-18)
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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 18-19)
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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 21-22)
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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 21-22)
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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 21-22)
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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:
- examples/read_recphyloxml_free_living_quadruple.rs
- examples/read_recphyloxml_copie.rs
- examples/read_recphyloxml_big_2.rs
- examples/read_recphyloxml_free_living_double.rs
- examples/read_recphyloxml_obsolete.rs
- examples/read_recphyloxml_switch.rs
- examples/read_recphyloxml_big.rs
- examples/read_recphyloxml_4.rs
- examples/read_recphyloxml_width_height.rs
- examples/read_recphyloxml_thickness_2.rs
- examples/read_recphyloxml_tidyspecies.rs
- examples/read_recphyloxml_2.rs
- examples/read_recphyloxml_thickness.rs
- examples/read_recphyloxml_stroke_thickness.rs
- examples/read_recphyloxml_3.rs
- examples/read_recphyloxml_multi.rs
- examples/read_recphyloxml_thirdlevel_5.rs
- examples/read_recphyloxml_thirdlevel_6.rs
- examples/read_recphyloxml_thirdlevel_bug.rs
- examples/read_recphyloxml_thirdlevel_1.rs
- examples/read_recphyloxml_thirdlevel_3.rs
- examples/read_recphyloxml_thirdlevel_1_midist.rs
- examples/read_recphyloxml_thirdlevel_2.rs
- examples/read_recphyloxml_thirdlevel_stroke.rs
- examples/read_recphyloxml_thirdlevel_fl.rs
- examples/read_recphyloxml_thirdlevel_alex.rs
- examples/read_recphyloxml_thirdlevel_4.rs
- examples/read_recphyloxml_thirdlevel_4_landscape.rs
- examples/read_recphyloxml.rs