use light_phylogeny::{ArenaTree,Options,Config,read_recphyloxml_multi,recphyloxml_processing,phyloxml_processing};
fn main() {
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/toyrec.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, "toy1.svg".to_string());
println!("Please open output file 'toy1.svg' with your browser");
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();
options.node_colors.push("m3".to_string());
options.node_colors.push("m35".to_string());
options.node_colors.push("m26".to_string());
options.gene_colors.push("black".to_string());
options.gene_colors.push("green".to_string());
options.gene_colors.push("blue".to_string());
options.gene_colors.push("orange".to_string());
read_recphyloxml_multi("examples/toyrec.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, "toy2.svg".to_string());
println!("Please open output file 'toy2.svg' with your browser");
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();
options.node_colors.push("m3".to_string());
options.node_colors.push("m35".to_string());
options.node_colors.push("m26".to_string());
options.node_colors.push("bidon".to_string());
read_recphyloxml_multi("examples/toyrec.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, "toy3.svg".to_string());
println!("Please open output file 'toy3.svg' with your browser");
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();
options.gene_colors.push("black".to_string());
options.gene_colors.push("green".to_string());
options.gene_colors.push("blue".to_string());
options.gene_colors.push("orange".to_string());
options.node_colors.push("03_duplication".to_string());
options.node_colors.push("b4_duplication".to_string());
read_recphyloxml_multi("examples/example_dupli.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, "dupli_color.svg".to_string());
println!("Please open output file 'dupli_color.svg' with your browser");
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();
options.node_colors.push("03_duplication".to_string());
options.node_colors.push("b4_duplication".to_string());
read_recphyloxml_multi("examples/example_dupli.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, "dupli_color2.svg".to_string());
println!("Please open output file 'dupli_color2.svg' with your browser");
}