// Display a reconciled tree form recPhyloXML format

use light_phylogeny::{ArenaTree,Options,Config,read_recphyloxml_multi,recphyloxml_processing};

fn main() {

    let transfers = vec![];
    let mut options: Options = Options::new();
    let mut config: Config = Config::new();
    options.height = 2.0;
    options.ratio = 1.5;
    // 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/gene_tree_HBG011000.newick_recs.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");

    // Version paysage
    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_tree_HBG011000.newick_recs.recphylo".to_string(),
        &mut sp_tree, &mut gene_trees, &mut global_roots);
    options.rotate = false;
    config.species_opacity = "0.3".to_string();
    config.gene_opacity = "0.6".to_string();
    recphyloxml_processing(&mut sp_tree, &mut gene_trees, &mut options, &config, true,
         &transfers, "read_recphyloxml_landscape.svg".to_string());
    println!("Please open output file 'read_recphyloxml_landscape.svg' with your browser");


    // // Version real_branch
    //
    // let transfers = vec![];
    // // Version pour  avec loption uniform etreal length
    // let mut options: Options = Options::new();
    // options.uniform = true;
    // options.real_length_flag = 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_tree_HBG011000.newick_recs.recphylo".to_string(),
    //     &mut sp_tree, &mut gene_trees, &mut global_roots);
    // let _pipeblock    = 15.0;
    // let min_dist = sp_tree.get_smallest_l();
    // // we want min_dist = _pipeblock
    // if min_dist == 0.0 {
    //     panic!("There is branch distance equal to 0.0");
    // }
    //
    // recphyloxml_processing(&mut sp_tree, &mut gene_trees, &mut options, &config, true,
    //      &transfers, "read_recphyloxml_real.svg".to_string());
    // println!("Please open output file 'read_recphyloxml_real.svg' with your browser");




}