Crate rectree2svg

rectree2svg

rectree2svg Read phylogenetic trees in newick, phyloxml or recPhyloXML format, build and manipulate phylogenetic trees, create svg representation of the tree with several options.

Structs

ArenaTree	Structure ArenaTree.
Noeud	Structure Noeud.
Options	Structure Options: drawing options.

Enums

Event

enum of the possible events in a gene tree

Functions

add_child	Add a node to another node
bilan_mappings	Shift the gene nodes in a given species node to avoid superposition.
center_gene_nodes	Center the gene nodes into a specie snode
check_contour_postorder	Solve the conflicts between the left subtree and the right subtree
check_for_obsolete	Processig potential obsolete tag from the old recPhyloXML format
check_is_rooted	Check is tree in newick format is rooted
check_vertical_contour_postorder	Solve the conflicts between a parent and its children
cladogramme	Transforms the tree into cladogram
close_chemin_sp	Finish the drawing of species tree at the leaves level.
draw_sptree_gntrees	Draw a svg pipe species tree and several gene trees inside it
draw_tree	Draw a svg simple tree
find_left_right	Split a parenthesed tree into left and right parenthsed trees and trailing string
find_rgtrees	Get the list of ids of all the “regGeneTree” tag in a xml document.
find_sptree	Get the id of the first “spTree” tag.
get_carre	Draw a square of size s at x,y
get_chemin_carre	Draw a square path between x1,y1 ad x2,y2
get_chemin_sp	Draw a square pipe path between x1,y1 ad x2,y2
get_chemin_transfer	Draw a transfer path between x1,y1 ad x2,y2
get_circle	Draw a circle of size s at x,y
get_contour_left	Get the left ‘contour’ of a sub tree
get_contour_right	Get the right ‘contour’ of a sub tree
get_cross	Draw a cross of size s at x,y
get_maxdepth	Get the depth of the tree
get_triangle	Draw a triangle of size s at x,y
knuth_layout	Set x and y of nodes : left son x is 0; right son x is 1; y is depth
lca	Send the index of the last common ancestor of 2 nodes
map_gene_trees	Set the coordinates of the gene tree according to species tree coordinates
map_species_trees	Determine the number of gene nodes associated to a species node
move_child	Move a node from a parent node to another node
move_dupli_mappings	Shift again the previously shifted gene nodes in case of a duplication node or a leaf
newick2tree	Fill an ArenaTree structure with the contents of a parentheses tree.
node_xpos	Get the leftest or rightest x value of a node
node_ypos	Get the upper or lower y value of a node
push_down	Check for conficts between parents and children and shift down nodes in order to solve detected conflicts ( for species pipe tree only).
push_right	Check for conficts between subtrees and shift conflicting right-hand subtrees to the right in order to solve detected conflicts.
real_length	Transforms the tree into real branch length representation
reset_pos	Reset the position of the tree
set_leaves_to_bottom	Set the y values of the leaves of the node index to max value
set_middle_postorder	Set the x of the father between its children
set_species_width	Set the width of the species tree pipe.
shift_mod_xy	Shift the x values of a node and its children according to the cumulated xmod values
summary	Display a short summary of each node of the tree
xml2tree	Fill an ArenaTree structure with the contents of a roxmltre::Node structure