Function light_phylogeny::map_transfer

source · 
pub fn map_transfer(
    transfers: Vec<(String, String)>,
    parasite_tree: &mut ArenaTree<String>
) -> Vec<(String, String)>
Expand description

Map a transfer in gene tree to the species tree.

Examples found in repository?
examples/read_recphyloxml_2.rs (line 87)
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fn main() {


    let mut options: Options = Options::new();
    let config: Config = Config::new();
    let transfers = vec![];
    let infile_gene_para = "examples/gene_parasite_page2.recphylo".to_string();
    let infile_para_host = "examples/hote_parasite_page2.recphylo".to_string();

    let outfile_gene_para = String::from("gene_para.svg");
    let outfile_para = String::from("para.svg");
    let outfile_para_rec = String::from("para_rec.svg");
    let outfile_para_host = String::from("para_host.svg");
    let outfile_host = String::from("host.svg");

    // On cree une structure Arena pour l'arbre d'espece
    // et un vecteur de  structures Arena pour le(s) arbres de gènes
    // -------------------------------------------------------------
    // Creation de la structure ArenaTree pour l'arbre d'espece
    // --------------------------------------------------------
    let mut tree_para_pipe: ArenaTree<String> = ArenaTree::default();
    // Creation du vecteur de structure ArenaTree pour les genes
    // ---------------------------------------------------------
    let mut gene_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
    let mut global_roots: std::vec::Vec<usize> = Vec::new();
    read_recphyloxml_multi(infile_gene_para,&mut tree_para_pipe,&mut gene_trees, &mut global_roots);
    let  nb_gntree =  gene_trees.len().clone();
    println!("Number of gene trees : {}",nb_gntree);
    info!("List of gene trees : {:?}",gene_trees);
    recphyloxml_processing(&mut tree_para_pipe,&mut  gene_trees, &mut options, &config,true,
        &transfers,outfile_gene_para);
    reset_pos(&mut tree_para_pipe);
    phyloxml_processing(&mut tree_para_pipe, &mut options, &config,outfile_para);

    // On cree une structure Arena pour l'arbre d'espece
    // et un vecteur de  structures Arena pour le(s) arbres de gènes
    // -------------------------------------------------------------
    // Creation de la structure ArenaTree pour l'arbre d'espece
    // --------------------------------------------------------
    let mut tree_host_pipe: ArenaTree<String> = ArenaTree::default();
    // Creation du vecteur de structure ArenaTree pour les genes
    // ---------------------------------------------------------
    let mut para_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
    let mut global_roots: std::vec::Vec<usize> = Vec::new();
    read_recphyloxml_multi(infile_para_host,&mut tree_host_pipe,&mut para_trees, &mut  global_roots);
    let  nb_paratree =  para_trees.len().clone();
    println!("Number of gene trees : {}",nb_paratree);
    info!("List of gene trees : {:?}",para_trees);
    recphyloxml_processing(&mut tree_host_pipe,&mut  para_trees, &mut options, &config,
        true, &transfers,outfile_para_host);
    reset_pos(&mut tree_host_pipe);
    phyloxml_processing(&mut tree_host_pipe, &mut options, &config,outfile_host);
    reset_pos(&mut para_trees[0]);
    phyloxml_processing(&mut para_trees[0], &mut options, &config,outfile_para_rec);

    // Generation du svg 3 niveaux
    println!("Parasite trees as a 'gene tree' : {:?}",para_trees);
    println!("Parasite tree as a 'species tree' : {:?}",tree_para_pipe);
    println!("Map parasite as 'gene' to parasite as 'species'");
    println!("==============================================");
    map_parasite_g2s(&mut tree_para_pipe, &mut para_trees[0]);
    println!("Map parasite as 'species' to paraiste as 'gene'");
    println!("==============================================");
    map_parasite_s2g(&mut tree_para_pipe, &mut para_trees[0], &mut gene_trees);
    println!("Mapping again!");
    println!("Map parasite as 'gene' to parasite as 'species'");
    println!("==============================================");
    map_parasite_g2s(&mut tree_para_pipe, &mut para_trees[0]);
    summary(&mut tree_para_pipe);

    reset_pos(&mut tree_para_pipe);
    reset_pos(&mut gene_trees[0]);
    recphyloxml_processing(&mut tree_para_pipe, &mut gene_trees, &mut options, &config, false,
        &transfers,"test_mapped.svg".to_string());

    // Generation des svg hote parsite  +transfert gene

    let gene_transfers = get_gtransfer(&mut gene_trees[0]);
    println!("Transfers = {:?}",gene_transfers);
    let mapped_gene_transfers = map_transfer(gene_transfers, &mut para_trees[0]);
    println!("Mapped transfers = {:?}",mapped_gene_transfers);
    reset_pos(&mut tree_host_pipe);
    reset_pos(&mut para_trees[0]);
    recphyloxml_processing(&mut tree_host_pipe, &mut para_trees, &mut options, &config,
        false, &mapped_gene_transfers,"test_mapped_2levels.svg".to_string());



}
More examples
Hide additional examples
examples/read_recphyloxml_3.rs (line 119)
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fn main() {


    let mut options: Options = Options::new();
    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_gene_para = "examples/recgs_dtl.recphyloxml".to_string();
    let infile_para_host = "examples/rechp_dtl.recphyloxml".to_string();

    // let infile_gene_para = "examples/gene_parasite_page4.recphylo".to_string();
    // let infile_para_host = "examples/hote_parasite_page4.recphylo".to_string();


    let outfile_gene_para = String::from("gene_para.svg");
    let outfile_para = String::from("para.svg");
    let outfile_para_rec = String::from("para_rec.svg");
    let outfile_para_host = String::from("para_host.svg");
    let outfile_host = String::from("host.svg");

    // On cree une structure Arena pour l'arbre d'espece
    // et un vecteur de  structures Arena pour le(s) arbres de gènes
    // -------------------------------------------------------------
    // Creation de la structure ArenaTree pour l'arbre d'espece
    // --------------------------------------------------------
    let mut tree_para_pipe: ArenaTree<String> = ArenaTree::default();
    // Creation du vecteur de structure ArenaTree pour les genes
    // ---------------------------------------------------------
    let mut gene_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
    let mut global_roots: std::vec::Vec<usize> = Vec::new();
    read_recphyloxml_multi(infile_gene_para, &mut tree_para_pipe, &mut gene_trees, &mut global_roots);
    let  nb_gntree =  gene_trees.len().clone();
    // let mut gene_trees_clone:std::vec::Vec<ArenaTree<String>> = Vec::new();
    // let mut i = 0;
    // while i < nb_gntree {
    //  gene_trees_clone.push(gene_trees[i].clone());
    // i = i + 1;
    // }
    println!("Number of gene trees : {}",nb_gntree);
    info!("List of gene trees : {:?}",gene_trees);
    recphyloxml_processing(&mut tree_para_pipe,&mut  gene_trees, &mut options, &config,true,
        &transfers,outfile_gene_para);
    reset_pos(&mut tree_para_pipe);
    phyloxml_processing(&mut tree_para_pipe, &mut options, &config,outfile_para);

    // On cree une structure Arena pour l'arbre d'espece
    // et un vecteur de  structures Arena pour le(s) arbres de gènes
    // -------------------------------------------------------------
    // Creation de la structure ArenaTree pour l'arbre d'espece
    // --------------------------------------------------------
    let mut tree_host_pipe: ArenaTree<String> = ArenaTree::default();
    // Creation du vecteur de structure ArenaTree pour les genes
    // ---------------------------------------------------------
    let mut para_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
    let mut global_roots: std::vec::Vec<usize> = Vec::new();
    read_recphyloxml_multi(infile_para_host,&mut tree_host_pipe,&mut para_trees, &mut global_roots);
    let  nb_paratree =  para_trees.len().clone();
    assert_eq!(nb_paratree,1,"I want only one parasite tree");
    println!("Number of gene trees : {}",nb_paratree);
    info!("List of gene trees : {:?}",para_trees);
    recphyloxml_processing(&mut tree_host_pipe,&mut  para_trees, &mut options, &config,
        true, &transfers,outfile_para_host);
    reset_pos(&mut tree_host_pipe);
    phyloxml_processing(&mut tree_host_pipe, &mut options, &config,outfile_host);
    reset_pos(&mut para_trees[0]);
    phyloxml_processing(&mut para_trees[0], &mut options, &config,outfile_para_rec);

    // Generation du svg 3 niveaux
    println!("Parasite trees as a 'gene tree' : {:?}",para_trees);
    println!("Parasite tree as a 'species tree' : {:?}",tree_para_pipe);
    println!("Map parasite as 'gene' to parasite as 'species'");
    println!("==============================================");
    map_parasite_g2s(&mut tree_para_pipe, &mut para_trees[0]);
    println!("Map parasite as 'species' to paraiste as 'gene'");
    println!("==============================================");
    map_parasite_s2g(&mut tree_para_pipe, &mut para_trees[0], &mut gene_trees);
    println!("MAP AGAIN!");
    println!("MON GROS DEBUG PARAPIPE1{:?}",&mut tree_para_pipe);
    println!("Map parasite as 'gene' to parasite as 'species'");
    println!("==============================================");
    map_parasite_g2s(&mut tree_para_pipe, &mut para_trees[0]);
    summary(&mut tree_para_pipe);


    reset_pos(&mut tree_para_pipe);
    let mut i = 0;
    while i < nb_gntree {
    reset_pos(&mut gene_trees[i]);
    i = i + 1;
    }
    // reset_pos(&mut gene_trees[0]);
    // reset_pos(&mut gene_trees[1]);
    // reset_pos(&mut gene_trees[2]);
    // reset_pos(&mut gene_trees[2]);
    // options.species_internal = true;
    // options.gene_internal = true;
//     options.verbose = true;
//     env::set_var("RUST_LOG", "info");
// env_logger::init();
// info!("Verbosity set to Info");

    // attention on ne remape pas
    recphyloxml_processing(&mut tree_para_pipe, &mut gene_trees, &mut options, &config, false,
        &transfers,"visu_3levels_1.svg".to_string());

    // Generation des svg hote parsite  +transfert gene

    let gene_transfers = get_gtransfer(&mut gene_trees[0]);
    println!("Transfers = {:?}",gene_transfers);
    let mut mapped_gene_transfers = map_transfer(gene_transfers, &mut para_trees[0]);
    println!("Mapped transfers = {:?}",mapped_gene_transfers);
    let mut i = 1;
    while i < nb_gntree {
        let gene_transfers = get_gtransfer(&mut gene_trees[i]);
        println!("Transfers = {:?}",gene_transfers);
        let mapped = map_transfer(gene_transfers, &mut para_trees[0]);
        println!("Mapped transfers = {:?}",mapped);
        for val in mapped {
            mapped_gene_transfers.push(val);
        }
        i = i + 1;
    }
    reset_pos(&mut tree_host_pipe);
    reset_pos(&mut para_trees[0]);
    // attention on ne remape pas
    recphyloxml_processing(&mut tree_host_pipe, &mut para_trees, &mut options, &config,
        false, &mapped_gene_transfers,"visu_3levels_2.svg".to_string());


    // mapping des gene sur les hotes via les parasites
    map_gene_host(&mut gene_trees, &mut para_trees, &mut tree_host_pipe);
    reset_pos(&mut tree_host_pipe);
    let mut i = 0;
    while i < nb_gntree {
        reset_pos(&mut gene_trees[i]);
        i = i + 1;
    }
    recphyloxml_processing(&mut tree_host_pipe, &mut gene_trees, &mut options, &config,
        true, &vec![],"visu_3levels_3.svg".to_string());
}
examples/read_recphyloxml_thirdlevel_5.rs (line 136)
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fn main() {


    let mut options: Options = Options::new();
    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/test4/gene_parasite_page4.recphylo".to_string();
    let infile_sh = "examples/test4/hote_parasite_page4.recphylo".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
// ---------------------------------------------------------
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
// ---------------------------------------------------------
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;
}
// attention on ne remape pas
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
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
// let mut i = 0;
// while i < nb_parasite_pipe {
// map_gene_host(&mut path_genes, &mut path_para_trees[i], &mut tree_host_pipe);
// i = i + 1;
// }
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;
}
recphyloxml_processing(&mut tree_host_pipe, &mut path_genes, &mut options, &config,
true, &vec![],"mapped_3.svg".to_string());
// 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!();
}
}
examples/read_recphyloxml_thirdlevel_6.rs (line 139)
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fn main() {
    // env::set_var("RUST_LOG", "info");
    // env_logger::init();

    let mut options: Options = Options::new();
    options.gene_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/rec0.recphyloxml".to_string();
    let infile_sh = "examples/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
// ---------------------------------------------------------
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
// ---------------------------------------------------------
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;
}
// attention on ne remape pas
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
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;
}

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!();
}
}
examples/read_recphyloxml_thirdlevel_bug.rs (line 140)
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fn main() {
    // env::set_var("RUST_LOG", "info");
    // env_logger::init();

    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/rec0.bug.recphyloxml".to_string();
    let infile_sh = "examples/rec0upper.bug.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
// ---------------------------------------------------------
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
// ---------------------------------------------------------
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;
}
// attention on ne remape pas
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
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;
}

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!();
}
}
examples/read_recphyloxml_thirdlevel_1.rs (line 139)
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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/recgs_mult_host_dtl.recphyloxml".to_string();
        let infile_gs = "examples/test1/recgs_dtl.recphyloxml".to_string();
    let infile_sh = "examples/test1/rechp_dtl.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
// ---------------------------------------------------------
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
// ---------------------------------------------------------
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;
}
// attention on ne remape pas
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
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;
}

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!();
}
}
Additional examples can be found in: