Bio::Phylo::Forest::DrawTreeRole(3)

NAME
Bio::Phylo::Forest::DrawTreeRole - Tree with extra methods for tree drawing

SYNOPSIS
 # see Bio::Phylo::Forest::Tree

DESCRIPTION
The object models a phylogenetic tree, a container of Bio::Phylo::For- est::Node objects. The tree object inherits from Bio::Phylo::Listable, so look there for more methods.

In addition, this subclass of the default tree object Bio::Phylo::Forest::Tree has getters and setters for drawing trees, e.g. font and text attributes, etc.

METHODS

  CONSTRUCTORS

new()
    Tree constructor.

     Type    : Constructor
     Title   : new
     Usage   : my $tree = Bio::Phylo::Forest::DrawTree->new;
     Function: Instantiates a Bio::Phylo::Forest::DrawTree object.
     Returns : A Bio::Phylo::Forest::DrawTree object.
     Args    : No required arguments.

  MUTATORS

set_width()
     Type    : Mutator
     Title   : set_width
     Usage   : $tree->set_width($width);
     Function: Sets width
     Returns : $self
     Args    : width

set_height()
     Type    : Mutator
     Title   : set_height
     Usage   : $tree->set_height($height);
     Function: Sets height
     Returns : $self
     Args    : height

set_node_radius()
     Type    : Mutator
     Title   : set_node_radius
     Usage   : $tree->set_node_radius($node_radius);
     Function: Sets node_radius
     Returns : $self
     Args    : node_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   : $tree->set_node_colour($node_colour);
     Function: Sets node_colour
     Returns : $self
     Args    : node_colour

set_node_shape()
     Type    : Mutator
     Title   : set_node_shape
     Usage   : $tree->set_node_shape($node_shape);
     Function: Sets node_shape
     Returns : $self
     Args    : node_shape

set_node_image()
     Type    : Mutator
     Title   : set_node_image
     Usage   : $tree->set_node_image($node_image);
     Function: Sets node_image
     Returns : $self
     Args    : node_image

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_branch_color()
     Type    : Mutator
     Title   : set_branch_color
     Usage   : $tree->set_branch_color($branch_color);
     Function: Sets branch_color
     Returns : $self
     Args    : branch_color

set_branch_shape()
     Type    : Mutator
     Title   : set_branch_shape
     Usage   : $tree->set_branch_shape($branch_shape);
     Function: Sets branch_shape
     Returns : $self
     Args    : branch_shape

set_branch_width()
     Type    : Mutator
     Title   : set_branch_width
     Usage   : $tree->set_branch_width($branch_width);
     Function: Sets branch width
     Returns : $self
     Args    : branch_width

set_branch_style()
     Type    : Mutator
     Title   : set_branch_style
     Usage   : $tree->set_branch_style($branch_style);
     Function: Sets branch style
     Returns : $self
     Args    : branch_style

set_font_face()
     Type    : Mutator
     Title   : set_font_face
     Usage   : $tree->set_font_face($font_face);
     Function: Sets font_face
     Returns : $self
     Args    : font face, Verdana, Arial, Serif

set_font_size()
     Type    : Mutator
     Title   : set_font_size
     Usage   : $tree->set_font_size($font_size);
     Function: Sets font_size
     Returns : $self
     Args    : Font size in pixels

set_font_style()
     Type    : Mutator
     Title   : set_font_style
     Usage   : $tree->set_font_style($font_style);
     Function: Sets font_style
     Returns : $self
     Args    : Font style, e.g. Italic

set_margin()
     Type    : Mutator
     Title   : set_margin
     Usage   : $tree->set_margin($margin);
     Function: Sets margin
     Returns : $self
     Args    : margin

set_margin_top()
     Type    : Mutator
     Title   : set_margin_top
     Usage   : $tree->set_margin_top($margin_top);
     Function: Sets margin_top
     Returns : $self
     Args    : margin_top

set_margin_bottom()
     Type    : Mutator
     Title   : set_margin_bottom
     Usage   : $tree->set_margin_bottom($margin_bottom);
     Function: Sets margin_bottom
     Returns : $self
     Args    : margin_bottom

set_margin_left()
     Type    : Mutator
     Title   : set_margin_left
     Usage   : $tree->set_margin_left($margin_left);
     Function: Sets margin_left
     Returns : $self
     Args    : margin_left

set_margin_right()
     Type    : Mutator
     Title   : set_margin_right
     Usage   : $tree->set_margin_right($margin_right);
     Function: Sets margin_right
     Returns : $self
     Args    : margin_right

set_padding()
     Type    : Mutator
     Title   : set_padding
     Usage   : $tree->set_padding($padding);
     Function: Sets padding
     Returns : $self
     Args    : padding

set_padding_top()
     Type    : Mutator
     Title   : set_padding_top
     Usage   : $tree->set_padding_top($padding_top);
     Function: Sets padding_top
     Returns : $self
     Args    : padding_top

set_padding_bottom()
     Type    : Mutator
     Title   : set_padding_bottom
     Usage   : $tree->set_padding_bottom($padding_bottom);
     Function: Sets padding_bottom
     Returns : $self
     Args    : padding_bottom

set_padding_left()
     Type    : Mutator
     Title   : set_padding_left
     Usage   : $tree->set_padding_left($padding_left);
     Function: Sets padding_left
     Returns : $self
     Args    : padding_left

set_padding_right()
     Type    : Mutator
     Title   : set_padding_right
     Usage   : $tree->set_padding_right($padding_right);
     Function: Sets padding_right
     Returns : $self
     Args    : padding_right

set_mode()
     Type    : Mutator
     Title   : set_mode
     Usage   : $tree->set_mode($mode);
     Function: Sets mode
     Returns : $self
     Args    : mode, e.g. 'CLADO' or 'PHYLO'

set_shape()
     Type    : Mutator
     Title   : set_shape
     Usage   : $tree->set_shape($shape);
     Function: Sets shape
     Returns : $self
     Args    : shape, e.g. 'RECT', 'CURVY', 'DIAG'

set_text_horiz_offset()
     Type    : Mutator
     Title   : set_text_horiz_offset
     Usage   : $tree->set_text_horiz_offset($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   : $tree->set_text_vert_offset($text_vert_offset);
     Function: Sets text_vert_offset
     Returns : $self
     Args    : text_vert_offset

  ACCESSORS

get_width()
     Type    : Accessor
     Title   : get_width
     Usage   : my $width = $tree->get_width();
     Function: Gets width
     Returns : width
     Args    : NONE

get_height()
     Type    : Accessor
     Title   : get_height
     Usage   : my $height = $tree->get_height();
     Function: Gets height
     Returns : height
     Args    : NONE

get_node_radius()
     Type    : Accessor
     Title   : get_node_radius
     Usage   : my $node_radius = $tree->get_node_radius();
     Function: Gets node_radius
     Returns : node_radius
     Args    : NONE

get_node_colour()
     Type    : Accessor
     Title   : get_node_colour
     Usage   : my $node_colour = $tree->get_node_colour();
     Function: Gets node_colour
     Returns : node_colour
     Args    : NONE

get_node_shape()
     Type    : Accessor
     Title   : get_node_shape
     Usage   : my $node_shape = $tree->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 = $tree->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 = $tree->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 = $tree->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 = $tree->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 = $tree->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 = $tree->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 = $tree->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 = $tree->get_font_style();
     Function: Gets font_style
     Returns : font_style
     Args    : NONE

get_margin()
     Type    : Accessor
     Title   : get_margin
     Usage   : my $margin = $tree->get_margin();
     Function: Gets margin
     Returns : margin
     Args    : NONE

get_margin_top()
     Type    : Accessor
     Title   : get_margin_top
     Usage   : my $margin_top = $tree->get_margin_top();
     Function: Gets margin_top
     Returns : margin_top
     Args    : NONE

get_margin_bottom()
     Type    : Accessor
     Title   : get_margin_bottom
     Usage   : my $margin_bottom = $tree->get_margin_bottom();
     Function: Gets margin_bottom
     Returns : margin_bottom
     Args    : NONE

get_margin_left()
     Type    : Accessor
     Title   : get_margin_left
     Usage   : my $margin_left = $tree->get_margin_left();
     Function: Gets margin_left
     Returns : margin_left
     Args    : NONE

get_margin_right()
     Type    : Accessor
     Title   : get_margin_right
     Usage   : my $margin_right = $tree->get_margin_right();
     Function: Gets margin_right
     Returns : margin_right
     Args    : NONE

get_padding()
     Type    : Accessor
     Title   : get_padding
     Usage   : my $padding = $tree->get_padding();
     Function: Gets padding
     Returns : padding
     Args    : NONE

get_padding_top()
     Type    : Accessor
     Title   : get_padding_top
     Usage   : my $padding_top = $tree->get_padding_top();
     Function: Gets padding_top
     Returns : padding_top
     Args    : NONE

get_padding_bottom()
     Type    : Accessor
     Title   : get_padding_bottom
     Usage   : my $padding_bottom = $tree->get_padding_bottom();
     Function: Gets padding_bottom
     Returns : padding_bottom
     Args    : NONE

get_padding_left()
     Type    : Accessor
     Title   : get_padding_left
     Usage   : my $padding_left = $tree->get_padding_left();
     Function: Gets padding_left
     Returns : padding_left
     Args    : NONE

get_padding_right()
     Type    : Accessor
     Title   : get_padding_right
     Usage   : my $padding_right = $tree->get_padding_right();
     Function: Gets padding_right
     Returns : padding_right
     Args    : NONE

get_mode()
     Type    : Accessor
     Title   : get_mode
     Usage   : my $mode = $tree->get_mode();
     Function: Gets mode
     Returns : mode
     Args    : NONE

get_shape()
     Type    : Accessor
     Title   : get_shape
     Usage   : my $shape = $tree->get_shape();
     Function: Gets shape
     Returns : shape
     Args    : NONE

get_text_horiz_offset()
     Type    : Accessor
     Title   : get_text_horiz_offset
     Usage   : my $text_horiz_offset = $tree->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 = $tree->get_text_vert_offset();
     Function: Gets text_vert_offset
     Returns : text_vert_offset
     Args    : NONE

SEE ALSO
There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.

Bio::Phylo::Forest::Tree
    This object inherits from Bio::Phylo::Forest::Tree, 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>