Index
- NAME
- SYNOPSIS
- DESCRIPTION
- METHODS
- MUTATORS
-
- set_collapsed()
- set_collapsed_clade_width()
- set_x()
- set_y()
- set_radius()
- set_tip_radius()
- set_node_colour()
- set_node_outline_colour()
- set_node_shape()
- set_node_image()
- set_branch_color()
- set_branch_shape()
- set_branch_width()
- set_branch_style()
- set_font_face()
- set_font_size()
- set_font_style()
- set_url()
- set_text_horiz_offset()
- set_text_vert_offset()
- ACCESSORS
-
- get_collapsed()
- get_first_daughter()
- get_last_daughter()
- get_children()
- get_x()
- get_y()
- get_radius()
- get_node_colour()
- get_node_outline_colour()
- get_node_shape()
- get_node_image()
- get_collapsed_clade_width()
- get_branch_color()
- get_branch_shape()
- get_branch_width()
- get_branch_style()
- get_font_face()
- get_font_size()
- get_font_style()
- get_url()
- get_text_horiz_offset()
- get_text_vert_offset()
- SERIALIZERS
- SEE ALSO
- CITATION
- REVISION
NAME
Bio::Phylo::Forest::DrawNode - Tree node with extra methods for tree drawing
SYNOPSIS
# see Bio::Phylo::Forest::Node
DESCRIPTION
This module defines a node object and its methods. The node is fairly syntactically rich in terms of navigation, and additional getters are provided to further ease navigation from node to node. Typical first daughter -> next sister traversal and recursion is possible, but there are also shrinkwrapped methods that return for example all terminal descendants of the focal node, or all internals, etc.
Node objects are inserted into tree objects, although technically the tree object is only a container holding all the nodes together. Unless there are orphans all nodes can be reached without recourse to the tree object.
In addition, this subclass of the default node object Bio::Phylo::Forest::Node has getters and setters for drawing trees and nodes, e.g. X/Y coordinates, font and text attributes, etc.
METHODS
MUTATORS
- set_collapsed()
-
Type : Mutator Title : set_collapsed Usage : $node->set_collapsed(1); Function: Sets whether the node's descendants are shown as collapsed into a triangle Returns : $self Args : true or false value
- set_collapsed_clade_width()
-
Sets collapsed clade width.
Type : Mutator Title : set_collapsed_clade_width Usage : $tree->set_collapsed_clade_width(6); Function: sets the width of collapsed clade triangles relative to uncollapsed tips Returns : Args : Positive number
- set_x()
-
Type : Mutator Title : set_x Usage : $node->set_x($x); Function: Sets x Returns : $self Args : x
- set_y()
-
Type : Mutator Title : set_y Usage : $node->set_y($y); Function: Sets y Returns : $self Args : y
- set_radius()
-
Type : Mutator Title : set_radius Usage : $node->set_radius($radius); Function: Sets radius Returns : $self Args : radius
- set_tip_radius()
-
Type : Mutator Title : set_tip_node_radius Usage : $tree->set_tip_radius($node_radius); Function: Sets tip radius Returns : $self Args : tip radius
- set_node_colour()
-
Type : Mutator Title : set_node_colour Usage : $node->set_node_colour($node_colour); Function: Sets node_colour Returns : $self Args : node_colour
- set_node_outline_colour()
-
Type : Mutator Title : set_node_outline_colour Usage : $node->set_node_outline_colour($node_outline_colour); Function: Sets node outline colour Returns : $self Args : node_colour
- set_node_shape()
-
Type : Mutator Title : set_node_shape Usage : $node->set_node_shape($node_shape); Function: Sets node_shape Returns : $self Args : node_shape
- set_node_image()
-
Type : Mutator Title : set_node_image Usage : $node->set_node_image($node_image); Function: Sets node_image Returns : $self Args : node_image
- set_branch_color()
-
Type : Mutator Title : set_branch_color Usage : $node->set_branch_color($branch_color); Function: Sets branch_color Returns : $self Args : branch_color
- set_branch_shape()
-
Type : Mutator Title : set_branch_shape Usage : $node->set_branch_shape($branch_shape); Function: Sets branch_shape Returns : $self Args : branch_shape
- set_branch_width()
-
Type : Mutator Title : set_branch_width Usage : $node->set_branch_width($branch_width); Function: Sets branch width Returns : $self Args : branch_width
- set_branch_style()
-
Type : Mutator Title : set_branch_style Usage : $node->set_branch_style($branch_style); Function: Sets branch style Returns : $self Args : branch_style
- set_font_face()
-
Type : Mutator Title : set_font_face Usage : $node->set_font_face($font_face); Function: Sets font_face Returns : $self Args : font_face
- set_font_size()
-
Type : Mutator Title : set_font_size Usage : $node->set_font_size($font_size); Function: Sets font_size Returns : $self Args : font_size
- set_font_style()
-
Type : Mutator Title : set_font_style Usage : $node->set_font_style($font_style); Function: Sets font_style Returns : $self Args : font_style
- set_url()
-
Type : Mutator Title : set_url Usage : $node->set_url($url); Function: Sets url Returns : $self Args : url
- set_text_horiz_offset()
-
Type : Mutator Title : set_text_horiz_offset Usage : $node->set_text_horiz_offset($text_horiz_offset); Function: Sets text_horiz_offset Returns : $self Args : text_horiz_offset
- set_text_vert_offset()
-
Type : Mutator Title : set_text_vert_offset Usage : $node->set_text_vert_offset($text_vert_offset); Function: Sets text_vert_offset Returns : $self Args : text_vert_offset
ACCESSORS
- get_collapsed()
-
Type : Mutator Title : get_collapsed Usage : something() if $node->get_collapsed(); Function: Gets whether the node's descendants are shown as collapsed into a triangle Returns : true or false value Args : NONE
- get_first_daughter()
-
Gets invocant's first daughter.
Type : Accessor Title : get_first_daughter Usage : my $f_daughter = $node->get_first_daughter; Function: Retrieves a node's leftmost daughter. Returns : Bio::Phylo::Forest::Node Args : NONE
- get_last_daughter()
-
Gets invocant's last daughter.
Type : Accessor Title : get_last_daughter Usage : my $l_daughter = $node->get_last_daughter; Function: Retrieves a node's rightmost daughter. Returns : Bio::Phylo::Forest::Node Args : NONE
- get_children()
-
Gets invocant's immediate children.
Type : Query Title : get_children Usage : my @children = @{ $node->get_children }; Function: Returns an array reference of immediate descendants, ordered from left to right. Returns : Array reference of Bio::Phylo::Forest::Node objects. Args : NONE - get_x()
-
Type : Accessor Title : get_x Usage : my $x = $node->get_x(); Function: Gets x Returns : x Args : NONE
- get_y()
-
Type : Accessor Title : get_y Usage : my $y = $node->get_y(); Function: Gets y Returns : y Args : NONE
- get_radius()
-
Type : Accessor Title : get_radius Usage : my $radius = $node->get_radius(); Function: Gets radius Returns : radius Args : NONE
- get_node_colour()
-
Type : Accessor Title : get_node_colour Usage : my $node_colour = $node->get_node_colour(); Function: Gets node_colour Returns : node_colour Args : NONE
- get_node_outline_colour()
-
Type : Accessor Title : get_node_outline_colour Usage : my $node_outline_colour = $node->get_node_outline_colour(); Function: Gets node outline colour Returns : node_colour Args : NONE
- get_node_shape()
-
Type : Accessor Title : get_node_shape Usage : my $node_shape = $node->get_node_shape(); Function: Gets node_shape Returns : node_shape Args : NONE
- get_node_image()
-
Type : Accessor Title : get_node_image Usage : my $node_image = $node->get_node_image(); Function: Gets node_image Returns : node_image Args : NONE
- get_collapsed_clade_width()
-
Gets collapsed clade width.
Type : Mutator Title : get_collapsed_clade_width Usage : $w = $tree->get_collapsed_clade_width(); Function: gets the width of collapsed clade triangles relative to uncollapsed tips Returns : Positive number Args : None
- get_branch_color()
-
Type : Accessor Title : get_branch_color Usage : my $branch_color = $node->get_branch_color(); Function: Gets branch_color Returns : branch_color Args : NONE
- get_branch_shape()
-
Type : Accessor Title : get_branch_shape Usage : my $branch_shape = $node->get_branch_shape(); Function: Gets branch_shape Returns : branch_shape Args : NONE
- get_branch_width()
-
Type : Accessor Title : get_branch_width Usage : my $branch_width = $node->get_branch_width(); Function: Gets branch_width Returns : branch_width Args : NONE
- get_branch_style()
-
Type : Accessor Title : get_branch_style Usage : my $branch_style = $node->get_branch_style(); Function: Gets branch_style Returns : branch_style Args : NONE
- get_font_face()
-
Type : Accessor Title : get_font_face Usage : my $font_face = $node->get_font_face(); Function: Gets font_face Returns : font_face Args : NONE
- get_font_size()
-
Type : Accessor Title : get_font_size Usage : my $font_size = $node->get_font_size(); Function: Gets font_size Returns : font_size Args : NONE
- get_font_style()
-
Type : Accessor Title : get_font_style Usage : my $font_style = $node->get_font_style(); Function: Gets font_style Returns : font_style Args : NONE
- get_url()
-
Type : Accessor Title : get_url Usage : my $url = $node->get_url(); Function: Gets url Returns : url Args : NONE
- get_text_horiz_offset()
-
Type : Accessor Title : get_text_horiz_offset Usage : my $text_horiz_offset = $node->get_text_horiz_offset(); Function: Gets text_horiz_offset Returns : text_horiz_offset Args : NONE
- get_text_vert_offset()
-
Type : Accessor Title : get_text_vert_offset Usage : my $text_vert_offset = $node->get_text_vert_offset(); Function: Gets text_vert_offset Returns : text_vert_offset Args : NONE
SERIALIZERS
- to_json()
-
Serializes object to JSON string
Type : Serializer Title : to_json() Usage : print $obj->to_json(); Function: Serializes object to JSON string Returns : String Args : None Comments:
SEE ALSO
- Bio::Phylo::Forest::Node
-
This object inherits from Bio::Phylo::Forest::Node, so methods defined there are also applicable here.
- Bio::Phylo::Manual
-
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
CITATION
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
REVISION
$Id: DrawNode.pm 1660 2011-04-02 18:29:40Z rvos $