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Man Pages


Manual Reference Pages  -  BIO::PHYLO::FOREST::DRAWTREEROLE (3)

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NAME

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

CONTENTS

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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::FOREST::DRAWTREEROLE (3) 2014-03-27

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