light_phylogeny/
lib.rs

1//! # light structures and functions for phylogeny
2//!
3//! `light_phylogeny` is a set of structures and functions dedicated to reading, building,
4//! manipulating and displaying phylogenic trees, especially reconciled trees  with speciation,
5//! duplication, loss and horizontal transfer events. Read newick, phyloXML and recPhyloXML files.
6//! For more information, visit <https://github.com/simonpenel/light_phylogeny/wiki>
7/// name = "light_phylogeny"
8/// version = "0.19.0"
9/// authors = ["Simon Penel <simon.penel@univ-lyon1.fr>"]
10/// license = "CECILL-2.1"
11mod arena;
12pub use self::arena::ArenaTree;
13pub use self::arena::Config;
14pub use self::arena::Event;
15pub use self::arena::Noeud;
16pub use self::arena::Options;
17
18pub use self::arena::add_child;
19pub use self::arena::bilan_mappings;
20pub use self::arena::bilan_mappings_reti;
21pub use self::arena::center_gene_nodes;
22pub use self::arena::check_contour_postorder;
23pub use self::arena::check_contour_postorder_tidy_tree;
24pub use self::arena::check_for_obsolete;
25pub use self::arena::check_is_rooted;
26pub use self::arena::check_vertical_contour_postorder;
27pub use self::arena::cladogramme;
28pub use self::arena::copie_fl;
29pub use self::arena::dmin_tidy;
30pub use self::arena::find_left_right;
31pub use self::arena::find_rgtrees;
32pub use self::arena::find_sptrees;
33pub use self::arena::fusion_mod_xy;
34pub use self::arena::get_contour_left;
35pub use self::arena::get_contour_right;
36pub use self::arena::get_contour_tidy_left;
37pub use self::arena::get_contour_tidy_right;
38pub use self::arena::get_maxdepth;
39pub use self::arena::knuth_layout;
40pub use self::arena::lca;
41pub use self::arena::map_gene_trees;
42pub use self::arena::map_species_trees;
43pub use self::arena::move_child;
44pub use self::arena::move_dupli_mappings;
45pub use self::arena::move_species_mappings;
46pub use self::arena::newick2tree;
47pub use self::arena::node_xpos;
48pub use self::arena::node_ypos;
49pub use self::arena::process_fl;
50pub use self::arena::push_down;
51pub use self::arena::push_right;
52pub use self::arena::push_right_tidy_tree;
53pub use self::arena::real_length;
54pub use self::arena::remplace_fl_inv;
55pub use self::arena::reset_pos;
56pub use self::arena::scale_heigth;
57pub use self::arena::scale_width;
58pub use self::arena::set_leaves_to_bottom;
59pub use self::arena::set_leaves_y_values;
60pub use self::arena::set_middle_postorder;
61pub use self::arena::set_species_width;
62pub use self::arena::shift_mod_xy;
63pub use self::arena::shift_nodes_y_values;
64pub use self::arena::species_uniformisation;
65pub use self::arena::summary;
66pub use self::arena::xml2tree;
67
68mod drawing;
69pub use self::drawing::close_chemin_sp;
70pub use self::drawing::close_chemin_sp_filled;
71pub use self::drawing::draw_sptree_gntrees;
72pub use self::drawing::draw_tree;
73pub use self::drawing::get_cadre;
74pub use self::drawing::get_carre;
75pub use self::drawing::get_chemin_carre;
76pub use self::drawing::get_chemin_sp;
77pub use self::drawing::get_chemin_sp_filled;
78pub use self::drawing::get_chemin_transfer;
79pub use self::drawing::get_circle;
80pub use self::drawing::get_cross;
81pub use self::drawing::get_default_color;
82pub use self::drawing::get_half_circle;
83pub use self::drawing::get_longest_name;
84pub use self::drawing::get_longest_name_mul;
85pub use self::drawing::get_longest_x_mul;
86pub use self::drawing::get_triangle;
87pub use self::drawing::set_color_index;
88
89mod building;
90pub use self::building::phyloxml_processing;
91pub use self::building::read_newick;
92pub use self::building::read_phyloxml;
93pub use self::building::read_recphyloxml_multi;
94pub use self::building::recphyloxml_processing;
95
96mod thirdlevel;
97pub use self::thirdlevel::get_gtransfer;
98pub use self::thirdlevel::map_gene_host;
99pub use self::thirdlevel::map_parasite_g2s;
100pub use self::thirdlevel::map_parasite_s2g;
101pub use self::thirdlevel::map_transfer;
102pub use self::thirdlevel::map_transfer_mul;
103pub use self::thirdlevel::select_transfer;
104#[cfg(test)]
105mod tests {
106    use super::*;
107
108    #[test]
109    fn check_set_event() {
110        let mut tree: ArenaTree<String> = ArenaTree::default();
111        let test = String::from("Test");
112        let index = tree.new_node(test);
113        let node = &mut tree.arena[index];
114        node.set_event(Event::Duplication);
115        assert_eq!(node.e, Event::Duplication);
116    }
117    #[test]
118    fn check_x_noref() {
119        let mut tree: ArenaTree<String> = ArenaTree::default();
120        let test = String::from("Test");
121        let index = tree.new_node(test);
122        let node = &mut tree.arena[index];
123        node.set_x_noref(10.0);
124        let x = node.x;
125        assert_eq!(x, 10.0);
126    }
127
128    #[test]
129    fn check_lca() {
130        let mut tree: ArenaTree<String> = ArenaTree::default();
131        let root = tree.new_node("root".to_string());
132        let a1 = tree.new_node("a1".to_string());
133        let a2 = tree.new_node("a2".to_string());
134        let a = tree.new_node("a".to_string());
135        let b = tree.new_node("b".to_string());
136        let c = tree.new_node("c".to_string());
137        let d = tree.new_node("d".to_string());
138        // Set hierarchy
139        //  a1 and a2 are children of a
140        tree.arena[a1].parent = Some(a);
141        tree.arena[a2].parent = Some(a);
142        tree.arena[a].children.push(a1);
143        tree.arena[a].children.push(a2);
144        // a and b are children of c
145        tree.arena[a].parent = Some(c);
146        tree.arena[b].parent = Some(c);
147        tree.arena[c].children.push(a);
148        tree.arena[c].children.push(b);
149        // c and d are children of root
150        tree.arena[c].parent = Some(root);
151        tree.arena[d].parent = Some(root);
152        tree.arena[root].children.push(c);
153        tree.arena[root].children.push(d);
154        let lca_test = lca(&mut tree, a1, b);
155        assert_eq!(lca_test, c);
156    }
157    #[test]
158    fn check_read_newick() {
159        let mut tree: ArenaTree<String> = ArenaTree::default();
160        read_newick("examples/newick.txt".to_string(), &mut tree);
161        let options: Options = Options::new();
162        let config: Config = Config::new();
163        phyloxml_processing(&mut tree, &options, &config, "toto.svg".to_string());
164    }
165    #[test]
166    fn check_read_recphylo() {
167        let mut sp_tree: ArenaTree<String> = ArenaTree::default();
168        let mut gene_trees: std::vec::Vec<ArenaTree<String>> = Vec::new();
169        let mut global_roots: std::vec::Vec<usize> = Vec::new();
170        let transfers = vec![];
171        let config: Config = Config::new();
172        let mut options: Options = Options::new();
173        read_recphyloxml_multi(
174            "recphylo_examples/FAM000297_reconciliated.recphylo".to_string(),
175            &mut sp_tree,
176            &mut gene_trees,
177            &mut global_roots,
178        );
179        recphyloxml_processing(
180            &mut sp_tree,
181            &mut gene_trees,
182            &mut options,
183            &config,
184            true,
185            &transfers,
186            "toto.svg".to_string(),
187        );
188        println!("Tree {:?}", sp_tree);
189    }
190    #[test]
191    fn check_read_phylo() {
192        let mut tree: ArenaTree<String> = ArenaTree::default();
193        let options: Options = Options::new();
194        let config: Config = Config::new();
195        read_phyloxml("examples/FAM036542_gene.xml".to_string(), &mut tree);
196        phyloxml_processing(
197            &mut tree,
198            &options,
199            &config,
200            "read_phyloxml.svg".to_string(),
201        );
202    }
203    #[test]
204    fn check_get_index() {
205        let mut tree: ArenaTree<String> = ArenaTree::default();
206        let index = tree.new_node("test".to_string());
207        tree.arena[index].name = "Test".to_string();
208        let test = tree
209            .get_index("Test".to_string())
210            .expect("Error in test check_get_index");
211        assert_eq!(test, index);
212    }
213}
light_phylogeny/lib.rs

light_phylogeny/
lib.rs
