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Bio-Phylo-v2.0.1
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Forest::DrawTreeRole

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