NAME

Bio::Graphics::Glyph - Base class for Bio::Graphics::Glyph objects

SYNOPSIS

DESCRIPTION

Bio::Graphics::Glyph is the base class for all glyph objects. Each glyph is a wrapper around an Bio:SeqFeatureI object, knows how to render itself on an Bio::Graphics::Panel, and has a variety of configuration variables.

End developers will not ordinarily work directly with Bio::Graphics::Glyph objects, but with Bio::Graphics::Glyph::generic and its subclasses. Similarly, most glyph developers will want to subclass from Bio::Graphics::Glyph::generic because the latter provides labeling and arrow-drawing facilities.

METHODS

This section describes the class and object methods for Bio::Graphics::Glyph.

CONSTRUCTORS

Bio::Graphics::Glyph objects are constructed automatically by an Bio::Graphics::Glyph::Factory, and are not usually created by end-developer code.

$glyph = Bio::Graphics::Glyph->new(-feature=>$feature,-factory=>$factory)

Given a sequence feature, creates an Bio::Graphics::Glyph object to display it. The -feature argument points to the Bio:SeqFeatureI object to display, and -factory indicates an Bio::Graphics::Glyph::Factory object from which the glyph will fetch all its run-time configuration information. Factories are created and manipulated by the Bio::Graphics::Panel object.

A standard set of options are recognized. See OPTIONS.

OBJECT METHODS

Once a glyph is created, it responds to a large number of methods. In this section, these methods are grouped into related categories.

Retrieving glyph context:

$factory = $glyph->factory: Get the Bio::Graphics::Glyph::Factory associated with this object. This cannot be changed once it is set.
$panel = $glyph->panel: Get the Bio::Graphics::Panel associated with this object. This cannot be changed once it is set.
$feature = $glyph->feature: Get the sequence feature associated with this object. This cannot be changed once it is set.
$feature = $glyph->add_feature(@features): Add the list of features to the glyph, creating subparts. This is most common done with the track glyph returned by Ace::Graphics::Panel->add_track().
$feature = $glyph->add_group(@features): This is similar to add_feature(), but the list of features is treated as a group and can be configured as a set.
$glyph->finished: When you are finished with a glyph, you can call its finished() method in order to break cycles that would otherwise cause memory leaks. finished() is typically only used by the Panel object.

Retrieving glyph options:

$fgcolor = $glyph->fgcolor
$bgcolor = $glyph->bgcolor
$fontcolor = $glyph->fontcolor
$fontcolor = $glyph->font2color
$fillcolor = $glyph->fillcolor: These methods return the configured foreground, background, font, alternative font, and fill colors for the glyph in the form of a GD::Image color index.
$color = $glyph->tkcolor: This method returns a color to be used to flood-fill the entire glyph before drawing (currently used by the "track" glyph).
$width = $glyph->width([$newwidth]): Return the width of the glyph, not including left or right padding. This is ordinarily set internally based on the size of the feature and the scale of the panel.
$width = $glyph->layout_width: Returns the width of the glyph including left and right padding.
$width = $glyph->height: Returns the height of the glyph, not including the top or bottom padding. This is calculated from the "height" option and cannot be changed.
$font = $glyph->font: Return the font for the glyph.
$option = $glyph->option($option): Return the value of the indicated option.
$index = $glyph->color($color): Given a symbolic or #RRGGBB-form color name, returns its GD index.
$level = $glyph->level: The "level" is the nesting level of the glyph. Groups are level -1, top level glyphs are level 0, subparts (e.g. exons) are level 1 and so forth.

Setting an option:

$glyph->configure(-name=>$value): You may change a glyph option after it is created using set_option(). This is most commonly used to configure track glyphs.

Retrieving information about the sequence:

$start = $glyph->start
$end = $glyph->end: These methods return the start and end of the glyph in base pair units.
$offset = $glyph->offset: Returns the offset of the segment (the base pair at the far left of the image).
$length = $glyph->length: Returns the length of the sequence segment.

Retrieving formatting information:

$top = $glyph->top
$left = $glyph->left
$bottom = $glyph->bottom
$right = $glyph->right: These methods return the top, left, bottom and right of the glyph in pixel coordinates.
$height = $glyph->height: Returns the height of the glyph. This may be somewhat larger or smaller than the height suggested by the GlyphFactory, depending on the type of the glyph.
$scale = $glyph->scale: Get the scale for the glyph in pixels/bp.
$height = $glyph->labelheight: Return the height of the label, if any.
$label = $glyph->label: Return a human-readable label for the glyph.

These methods are called by Bio::Graphics::Track during the layout process:

$glyph->move($dx,$dy): Move the glyph in pixel coordinates by the indicated delta-x and delta-y values.
($x1,$y1,$x2,$y2) = $glyph->box: Return the current position of the glyph.

These methods are intended to be overridden in subclasses:

$glyph->calculate_height

Calculate the height of the glyph.

$glyph->calculate_left

Calculate the left side of the glyph.

$glyph->calculate_right

Calculate the right side of the glyph.

$glyph->draw($gd,$left,$top)

Optionally offset the glyph by the indicated amount and draw it onto the GD::Image object.

$glyph->draw_label($gd,$left,$top)

Draw the label for the glyph onto the provided GD::Image object, optionally offsetting by the amounts indicated in $left and $right.

$glyph->maxdepth()

This returns the maximum number of levels of feature subparts that the glyph will recurse through. For example, returning 0 indicates that the glyph will only draw the top-level feature. Returning 1 indicates that it will only draw the top-level feature and one level of subfeatures. Returning 2 will descend down two levels. Overriding this method will speed up rendering by avoiding creating of a bunch of subglyphs that will never be drawn.

The default behavior is to return undef (unlimited levels of descent) unless the -maxdepth option is passed, in which case this number is returned.

Note that Bio::Graphics::Glyph::generic overrides maxdepth() to return 0, meaning no descent into subparts will be performed.

These methods are useful utility routines:

$pixels = $glyph->map_pt($bases);: Map the indicated base position, given in base pair units, into pixels, using the current scale and glyph position.
$glyph->filled_box($gd,$x1,$y1,$x2,$y2): Draw a filled rectangle with the appropriate foreground and fill colors, and pen width onto the GD::Image object given by $gd, using the provided rectangle coordinates.
$glyph->filled_oval($gd,$x1,$y1,$x2,$y2): As above, but draws an oval inscribed on the rectangle.
$glyph->exceeds_depth: Returns true if descending into another level of subfeatures will exceed the value returned by maxdepth().

OPTIONS

The following options are standard among all Glyphs. See individual glyph pages for more options.

Option      Description                      Default
------      -----------                      -------

-fgcolor      Foreground color	       black

-outlinecolor	Synonym for -fgcolor

-bgcolor      Background color               turquoise

-fillcolor    Synonym for -bgcolor

-linewidth    Line width                     1

-height       Height of glyph		       10

-font         Glyph font		       gdSmallFont

-connector    Connector type                 undef (false)

-connector_color
              Connector color                black

-strand_arrow Whether to indicate            undef (false)
               strandedness

-label        Whether to draw a label	       undef (false)

-description  Whether to draw a description  undef (false)

-no_subparts  Set to true to prevent         undef (false)
              drawing of the subparts
              of a feature.

-ignore_sub_part Give the types/methods of   undef
              subparts to ignore (as a 
              space delimited list).

-maxdepth     Specifies the maximum number   undef (unlimited) 
              child-generations to decend
              when getting subfeatures

-sort_order   Specify layout sort order      "default"

-always_sort  Sort even when bumping is off  undef (false)

-bump_limit   Maximum number of levels to bump undef (unlimited)

-hilite       Highlight color                undef (no color)

-link, -title, -target
             These options are used when creating imagemaps
             for display on the web.  See L<Bio::Graphics::Panel/"Creating Imagemaps">.

-filter      Select which features to
             display. Must be a CODE reference.

For glyphs that consist of multiple segments, the -connector option controls what's drawn between the segments. The default is undef (no connector). Options include:

"hat"     an upward-angling conector
"solid"   a straight horizontal connector
"quill"   a decorated line with small arrows indicating strandedness
          (like the UCSC Genome Browser uses)
"dashed"  a horizontal dashed line.
"crossed" a straight horizontal connector with an "X" on it
           (Can be used when segments are not yet validated
            by some internal experiments...)

The -connector_color option controls the color of the connector, if any.

The label is printed above the glyph. You may pass an anonymous subroutine to -label, in which case the subroutine will be invoked with the feature as its single argument. and is expected to return the string to use as the description. If you provide the numeric value "1" to -description, the description will be read off the feature's seqname(), info() and primary_tag() methods will be called until a suitable name is found. To create a label with the text "1", pass the string "1 ". (A 1 followed by a space).

The description is printed below the glyph. You may pass an anonymous subroutine to -description, in which case the subroutine will be invoked with the feature as its single argument and is expected to return the string to use as the description. If you provide the numeric value "1" to -description, the description will be read off the feature's source_tag() method. To create a description with the text "1", pass the string "1 ". (A 1 followed by a space).

In the case of ACEDB Ace::Sequence feature objects, the feature's info(), Brief_identification() and Locus() methods will be called to create a suitable description.

The -strand_arrow option, if true, requests that the glyph indicate which strand it is on, usually by drawing an arrowhead. Not all glyphs will respond to this request. For historical reasons, -stranded is a synonym for this option.

sort_order: By default, features are drawn with a layout based only on the position of the feature, assuring a maximal "packing" of the glyphs when bumped. In some cases, however, it makes sense to display the glyphs sorted by score or some other comparison, e.g. such that more "important" features are nearer the top of the display, stacked above less important features. The -sort_order option allows a few different built-in values for changing the default sort order (which is by "left" position): "low_score" (or "high_score") will cause features to be sorted from lowest to highest score (or vice versa). "left" (or "default") and "right" values will cause features to be sorted by their position in the sequence. "longer" (or "shorter") will cause the longest (or shortest) features to be sorted first, and "strand" will cause the features to be sorted by strand: "+1" (forward) then "0" (unknown, or NA) then "-1" (reverse).

In all cases, the "left" position will be used to break any ties. To break ties using another field, options may be strung together using a "|" character; e.g. "strand|low_score|right" would cause the features to be sorted first by strand, then score (lowest to highest), then by "right" position in the sequence.

Finally, a subroutine coderef with a $$ prototype can be provided. It will receive two glyph as arguments and should return -1, 0 or 1 (see Perl's sort() function for more information). For example, to sort a set of database search hits by bits (stored in the features' "score" fields), scaled by the log of the alignment length (with "start" position breaking any ties):

sort_order = sub ($$) {
  my ($glyph1,$glyph2) = @_;
  my $a = $glyph1->feature;
  my $b = $glyph2->feature;
  ( $b->score/log($b->length)
        <=>
    $a->score/log($a->length) )
        ||
  ( $a->start <=> $b->start )
}

It is important to remember to use the $$ prototype as shown in the example. Otherwise Bio::Graphics will quit with an exception. The arguments are subclasses of Bio::Graphics::Glyph, not the features themselves. While glyphs implement some, but not all, of the feature methods, to be safe call the two glyphs' feature() methods in order to convert them into the actual features.

The '-always_sort' option, if true, will sort features even if bumping is turned off. This is useful if you would like overlapping features to stack in a particular order. Features towards the end of the list will overlay those towards the beginning of the sort order.

The -hilite option draws a colored box behind each feature using the indicated color. Typically you will pass it a code ref that returns a color name. For example:

-hilite => sub { my $name = shift->display_name; 
                 return 'yellow' if $name =~ /XYZ/ }

The -no_subparts option will prevent the glyph from searching its feature for subfeatures. This may enhance performance if you know in advance that none of your features contain subfeatures.

The -filter option, which must be a CODE reference, will be invoked once for each feature prior to rendering it. The coderef will receive the feature as its single option and should return true if the feature is to be shown and false otherwise.

SUBCLASSING Bio::Graphics::Glyph

By convention, subclasses are all lower-case. Begin each subclass with a preamble like this one:

package Bio::Graphics::Glyph::crossbox;

use strict;
use base qw(Bio::Graphics::Glyph);

Then override the methods you need to. Typically, just the draw() method will need to be overridden. However, if you need additional room in the glyph, you may override calculate_height(), calculate_left() and calculate_right(). Do not directly override height(), left() and right(), as their purpose is to cache the values returned by their calculating cousins in order to avoid time-consuming recalculation.

A simple draw() method looks like this:

sub draw {
 my $self = shift;
 $self->SUPER::draw(@_);
 my $gd = shift;

 # and draw a cross through the box
 my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);
 my $fg = $self->fgcolor;
 $gd->line($x1,$y1,$x2,$y2,$fg);
 $gd->line($x1,$y2,$x2,$y1,$fg);
}

This subclass draws a simple box with two lines criss-crossed through it. We first call our inherited draw() method to generate the filled box and label. We then call calculate_boundaries() to return the coordinates of the glyph, disregarding any extra space taken by labels. We call fgcolor() to return the desired foreground color, and then call $gd->line() twice to generate the criss-cross.

For more complex draw() methods, see Bio::Graphics::Glyph::transcript and Bio::Graphics::Glyph::segments.

Please avoid using a specific image class (via "use GD" for example) within your glyph package. Instead, rely on the image package passed to the draw() method. This approach allows for future expansion of supported image classes without requiring glyph redesign. If you need access to the specific image classes such as Polygon, Image, or Font, generate them like such:

sub draw {
 my $self = shift;
 my $image_class = shift;

 my $polygon_package = $self->polygon_package->new()
 ...
 }

BUGS

Please report them.

AUTHOR

Lincoln Stein <lstein@cshl.org>

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

To install Bio::Seq, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Seq

CPAN shell

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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