Crate rectree2svg

tree2svg

tree2svg Read a phylogentic trees in newick, phyloxml or recPhyloXML format and create a svg.

Structs

ArenaTree	Structure ArenaTree.
Noeud	Structure Noeud.
Options

Enums

Event

enum of the possible events in a gene tree

Functions

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_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
knuth_layout	Set x and y of nodes : left son x is 0; right son x is 1; y is depth
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_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
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
xml2tree	Fill an ArenaTree structure with the contents of a roxmltre::Node structure