Crate light_phylogeny

light structures and functions for phylogeny

light_phylogeny is a set of structures and functions dedicated to reading, building, manipulating and displaying phylogenic trees, especially reconciled trees with speciation, duplication, loss and horizontal transfer events. Read newick, phyloXML and recPhyloXML files. For more information, visit https://github.com/simonpenel/light_phylogeny/wiki

Structs

• ArenaTree
  ArenaTree Structure. It describes a binary phylogenetic tree.
• Config
  Structure Config: drawing config.
• Noeud
  Noeud Structure. It describes a node of a tree stored in a Arena structure. Concerning recPhyloXML file, we assume in the documentation that it describes a gene/species reconciliation.
• Options
  Structure Options: these are the drawing options for the svg. Concerning recPhyloXML file, we assume in the documentation that it describes a gene/species reconciliation.

Enums

• Event
  Enum of the possible events in a gene tree.

Functions

• add_child
  Add a node to another node in a tree.
• bilan_mappings
  Shift the gene nodes in a given species node to avoid superposition.
• center_gene_nodes
  Center the gene nodes into a species node.
• check_contour_postorder
  Solve the conflicts between the left subtree and the right subtree.
• check_contour_postorder_tidy_tree
  Solve the conflicts between the left subtree and the right subtree.
• check_for_obsolete
  Processing potential obsolete tags from the old recPhyloXML format.
• check_is_rooted
  Check if tree in newick format is rooted.
• check_vertical_contour_postorder
  Solve the conflicts between a parent and its children in a tree (species pipe tree only).
• cladogramme
  Transforms the tree into cladogram.
• close_chemin_sp
  Finish the drawing of species tree at the leaves level.
• copie_fl
  Copy a node of the free-living part of a gene tree into a another tree under some conditions.
• dmin_tidy
  Get the minimal distance between 2 contours in “tidy” context.
• draw_sptree_gntrees
  Draw a svg pipe species tree and several gene trees inside it.
• draw_tree
  Draw the svg of a simple tree.
• find_left_right
  Split a parenthesed tree into left and right parenthesed trees and trailing string.
• find_rgtrees
  Get the list of ids of all the “regGeneTree” tag in a xml document.
• find_sptrees
  Get the list of ids of all the “spTree” tag in a xml document.
• get_cadre
  Draw a frame.
• get_carre
  Draw a square of size s at x,y.
• get_chemin_carre
  Draw a square path between x1,y1 and 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 and 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_contour_tidy_left
  Get the left ‘contour’ of a sub tree in the “tidy” context.
• get_contour_tidy_right
  Get the right ‘contour’ of a sub tree in the “tidy” context.
• get_cross
  Draw a cross of size s at x,y.
• get_default_color
  Get the default color in function of index
• get_gtransfer
  Get the transfers in a gene tree.
• get_half_circle
  Draw a half circle of size s at x,y.
• get_longest_name
  Get the longest node name in a tree.
• get_longest_name_mul
  Get the longest node name in a set of trees.
• get_longest_x_mul
  Get the largest x in set of trees.
• get_maxdepth
  Get the depth of a tree.
• get_triangle
  Draw a triangle of size s at x,y.
• knuth_layout
  Initial set x and y of nodes in a tree: 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_host
  Map gene trees to a host tree.
• map_gene_trees
  Set the coordinates of the gene tree according to the associated species tree coordinates.
• map_parasite_g2s
  Map a reconciled species tree to a pipe species tree.
• map_parasite_s2g
  Map a pipe species tree to a reconciled species tree.
• map_species_trees
  Determine and set the number of gene nodes associated to a species node.
• map_transfer
  Map a transfer in gene tree to the species tree.
• map_transfer_mul
  Map a transfer from a gene tree to the species trees.
• move_child
  Move a node from a parent node to another node in a tree.
• move_dupli_mappings
  Shift again previously shifted gene nodes in a species node in case of a duplication node or a leaf.
• move_species_mappings
  Move species father when the father and children of a gene speciation are in the same node tree (Only occurs for 3-level gene/symbiot/host reconciliation).
• 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
• phyloxml_processing
  Create a svg of the tree in phyloxml context.
• process_fl
  Specific processing of free living gene trees.
• push_down
  Check for conficts between parents and children and shift down nodes in order to solve detected conflicts (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.
• push_right_tidy_tree
  Check for conficts between subtrees and shift conflicting right-hand subtrees to the right in order to solve detected conflicts in the “tidy” context.
• read_newick
  Read a newick file and store the tree into ArenaTree structure.
• read_phyloxml
  Read a phyloxml file and store the tree into a ArenaTree structure.
• read_recphyloxml_multi
  Read a recphyloxml file and store the species and gene trees into several ArenaTree structures.
• real_length
  Use real branch lengths to build the tree.
• recphyloxml_processing
  Create a svg of the tree in recphyloxml context.
• remplace_fl_inv
  Replace the free-living part of a gene tree by a free living tree calculated independantly.
• reset_pos
  Reset all positions x y xmod ymod of a tree.
• scale_heigth
  Scaling tree height.
• scale_width
  Scaling tree width.
• select_transfer
  Get the transfers in a gene tree.
• set_color_index
  Set to idx the color_node_idx field of the children of root in gene_tree
• set_leaves_to_bottom
  Set the y values of the leaves of a tree to the same value in a cladogram.
• set_leaves_y_values
  Set the y values of the leaves of a tree to the same value in a real length branch tree.
• set_middle_postorder
  Set the x of the father between its children.
• set_species_width
  Set the node widths of the species tree pipe.
• shift_mod_xy
  Shift the x y values of a node and its children according to the cumulated xmod ymod values.
• shift_nodes_y_values
  Shift the y values of the nodes of a tree.
• species_uniformisation
  Uniformise the size of the pipe tree nodes (by uniformising nbg).
• summary
  Display a short summary of each node of a tree.
• xml2tree
  Fill an ArenaTree structure with the contents of a roxmltree::Node structure.