// Display a reconciled tree form recPhyloXML format

use light_phylogeny::{ArenaTree,Options,Config,read_recphyloxml_multi,recphyloxml_processing,phyloxml_processing};
// use std::env;

fn main() {

    // ============================================================================================
    // Version portrait
    let transfers = vec![];
    let mut options: Options = Options::new();
    options.species_internal = true ;
    options.uniform = false ;
    //options.switches.push("species_3".to_string());
    options.hybrid.push(("PBIAU".to_string(),"PTETRD4".to_string()));
    options.hybrid.push(("PQUAD".to_string(),"PNOVA".to_string()));



    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("recphylo_examples/FAM000600_reconciliated_big.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, "example_reti.svg".to_string());
    println!("Please open output file 'example_reti.svg' with your browser");


}