// Visualisation  of  3 levels reconciliation
//  Case there are several gene trees

use light_phylogeny::{ArenaTree,Options,Config,read_recphyloxml_multi,recphyloxml_processing,
phyloxml_processing,reset_pos,map_transfer,map_transfer_mul,get_gtransfer,map_parasite_g2s,
map_parasite_s2g,map_gene_host};
use log::{info};

fn main() {


    let mut options: Options = Options::new();
    options.gene_internal = true;
    options.species_internal = true;
    let mut config: Config = Config::new();
    config.species_opacity = "0.7".to_string();
    config.gene_opacity = "0.9".to_string();
    let transfers = vec![];
    let infile_gs = "examples/test5/rec0u_0_best.recphyloxml".to_string();
    let infile_sh = "examples/test5/rec0upper.recphyloxml".to_string();
    // Traitement de 2 fichier fichiers recPhyloXML
    println!("Two reconciled files => displaying 3-levels reconciliations. ");
    let  outfile_gene_para = String::from("gene_para.svg");
    let  outfile_para_host = String::from("para_host.svg");
    let  outfile_mapped_1 = String::from("mapped_1.svg");
    let  outfile_mapped_2 = String::from("mapped_2.svg");

// ---------------------------------------------------------
// Create a structure Arena for the global parasite pipe
// tree and a vector of structures Arena for gene path trees
// ---------------------------------------------------------
let mut global_pipe_parasite: ArenaTree<String> = ArenaTree::default();
let mut global_roots: std::vec::Vec<usize> = Vec::new();
let mut path_genes: std::vec::Vec<ArenaTree<String>> = Vec::new();
// ---------------------------------------------------------
// Fill global parasite pipe tree and is roots and path
// genes trees
// ---------------------------------------------------------
read_recphyloxml_multi(infile_gs,&mut global_pipe_parasite,&mut path_genes,&mut global_roots);
let  nb_gntree =  path_genes.len().clone();
println!("Number of gene trees : {}",nb_gntree);
info!("List of gene trees : {:?}",path_genes);
let  nb_parasite_pipe =  global_roots.len().clone();
println!("Number of parasite trees : {}",nb_parasite_pipe);
println!("List of species trees roots : {:?}",global_roots);
info!("Global parasite pipe tree : {:?}",global_pipe_parasite);
// ---------------------------------------------------------
// Generate svg of the lobal parasite pipe tree and  path
// genes trees
// ---------------------------------------------------------
// Setting options.free_living to false for parasite/gene processing
options.free_living = false;
recphyloxml_processing(&mut global_pipe_parasite,&mut  path_genes, &mut options, &config,true,
    &transfers,outfile_gene_para);
// ---------------------------------------------------------
// Create a structure Arena for the host pipe tree and a
// vector of structures Arena for parasite path trees
// ---------------------------------------------------------
let mut tree_host_pipe: ArenaTree<String> = ArenaTree::default();
let mut path_para_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
// ---------------------------------------------------------
// Fill  host pipe tree and is roots and path parasite trees
// ---------------------------------------------------------
let mut global_roots: std::vec::Vec<usize> = Vec::new();
read_recphyloxml_multi(infile_sh,&mut tree_host_pipe,&mut path_para_trees, &mut global_roots);
let  nb_parasite_path =  path_para_trees.len().clone();
println!("Number of pipe parasite trees in gene-parasite file : {}",nb_parasite_pipe);
println!("Number of path parasite trees in parasite-host file : {}",nb_parasite_path);
if nb_parasite_path != nb_parasite_pipe {
println!();
println!("==============================================");
println!("Error! Different number of parasite trees in the 2 files!");
println!("       Resulting svg will be incomplete.");
println!("==============================================");
println!();
}
// ---------------------------------------------------------
// Generate svg of the host pipe tree and path parasite trees
// ---------------------------------------------------------
// Setting options.free_living to true for host/parasite processing
options.free_living = true;
recphyloxml_processing(&mut tree_host_pipe,&mut  path_para_trees, &mut options, &config,
true, &transfers,outfile_para_host);
// ---------------------------------------------------------
// Generation of first 3 levels svg
// ---------------------------------------------------------
info!("Parasite trees as a 'path tree' : {:?}",path_para_trees);
info!("Parasite tree as a 'pipe tree' : {:?}",global_pipe_parasite);
println!("==============================================");
println!("Map parasite as 'path' to parasite as 'pipe'");
println!("==============================================");
let mut i = 0;
while i < nb_parasite_pipe {
    map_parasite_g2s(&mut global_pipe_parasite, &mut path_para_trees[i]);
i = i + 1;
}
info!("Global parasite tree wih events : {:?}",global_pipe_parasite);
reset_pos(&mut global_pipe_parasite);
let mut i = 0;
while i < nb_gntree {
reset_pos(&mut path_genes[i]);
i = i + 1;
}
println!("==============================================");
println!("Map parasite as 'species' to parasite as 'gene'");
println!("==============================================");
let mut i = 0;
while i < nb_parasite_pipe {
map_parasite_s2g(&mut global_pipe_parasite, &mut path_para_trees[i],&mut path_genes);
i = i +  1;
}
info!("Global pipe parasite after mapping s2g : {:?}",global_pipe_parasite);
println!("==============================================");
println!("Map parasite as 'gene' to parasite as 'species' again");
println!("==============================================");
let mut i = 0;
while i < nb_parasite_pipe {
map_parasite_g2s(&mut global_pipe_parasite, &mut path_para_trees[i]);
i = i + 1;
}
reset_pos(&mut global_pipe_parasite);
let mut i = 0;
while i < nb_gntree {
reset_pos(&mut path_genes[i]);
i = i + 1;
}
// options.free_living = false;
// attention on ne remape pas
options.free_living = false;
recphyloxml_processing(&mut global_pipe_parasite,&mut  path_genes, &mut options, &config,false,
    &transfers,outfile_mapped_1);
// ---------------------------------------------------------
// Generation of second 3 levels svg
// ---------------------------------------------------------
let mut i = 0;
let gene_transfers = get_gtransfer(&mut path_genes[i]);
info!("Transfers = {:?}",gene_transfers);
let mut mapped_gene_transfers = map_transfer_mul(gene_transfers, &mut path_para_trees);
info!("Mapped transfers = {:?}",mapped_gene_transfers);
i = i + 1;
while i < nb_gntree {
let gene_transfers = get_gtransfer(&mut path_genes[i]);
info!("Transfers = {:?}",gene_transfers);
let mapped = map_transfer(gene_transfers, &mut path_para_trees[0]);
info!("Mapped transfers = {:?}",mapped);
for val in mapped {
    mapped_gene_transfers.push(val);
}
i = i + 1;
}
reset_pos(&mut tree_host_pipe);
let mut i = 0;
while i < nb_parasite_pipe {
reset_pos(&mut path_para_trees[i]);
i = i + 1;
}
println!("Building svg 2:  parasite tree within host pipe tree and mapped tarnsfers {}",
outfile_mapped_2);
// attention on ne remape pas
options.free_living = true;
recphyloxml_processing(&mut tree_host_pipe, &mut path_para_trees, &mut options, &config,
false, &mapped_gene_transfers,outfile_mapped_2);
reset_pos(&mut global_pipe_parasite);
phyloxml_processing(&mut global_pipe_parasite, &mut options, &config,"para_simple.svg".to_string());
reset_pos(&mut tree_host_pipe);
phyloxml_processing(&mut tree_host_pipe, &mut options, &config,"host_simple.svg".to_string());
let mut i = 0;
while i < nb_parasite_pipe {
reset_pos(&mut path_para_trees[i]);
phyloxml_processing(&mut path_para_trees[i], &mut options, &config,("gene_simple_".to_owned()+&i.to_string()+".svg").to_string());
i = i + 1;
}

//llmlmlmlmlmlm
// mapping des gene sur les hotes via les parasites
println!("Building svg 3: gene  tree within host pipe tree");
map_gene_host(&mut path_genes, &mut path_para_trees, &mut tree_host_pipe);

// map_gene_host(&mut path_genes, &mut path_para_trees[1], &mut tree_host_pipe);
reset_pos(&mut tree_host_pipe);
let mut i = 0;
while i < nb_gntree {
reset_pos(&mut path_genes[i]);
i = i + 1;
}
options.free_living = false;
recphyloxml_processing(&mut tree_host_pipe, &mut path_genes, &mut options, &config,
true, &vec![],"mapped_3.svg".to_string());
// println!("DEBUG  FINAL HOST = {:?}",tree_host_pipe);
// lmlmlmlm

println!("Output files:");

println!(" - host_simple.svg ...... 1 level: host tree");
let mut i = 0;
while i < nb_parasite_pipe {
println!(" - para_simple.svg ...... 2 levels: gene_simple_{}.svg",&i);
i = i + 1;
}
println!(" - para_simple.svg ...... 2 levels: parasite tree(s)");
println!(" - gene_para.svg ........ 2 levels: pipe parasite tree(s) with gene tree(s) inside");
println!(" - para_host.svg ........ 2 levels: pipe host tree with parasite tree(s) inside");
println!(" - mapped_1.svg ........  3 levels: reconciled pipe parasite tree(s) with gene tree(s)");
println!(" - mapped_2.svg ........  3 levels: parasite-host reconciliation plus gene transfers");
println!(" - mapped_3.svg ........  3 levels: pipe host tree with gene tree(s) inside");

if nb_parasite_path != nb_parasite_pipe {
println!();
println!("==============================================");
println!("Error! Different number of parasite trees in the 2 files!");
println!("       Resulting svg will be incomplete.");
println!("==============================================");
println!();
}
}