Bio::Graphics::Glyph(3User Contributed Perl DocumentatiBio::Graphics::Glyph(3)NAMEBio::Graphics::Glyph - Base class for Bio::Graphics::Glyph objects
SYNOPSIS
See Bio::Graphics::Panel.
DESCRIPTIONBio::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->parent_feature()
Within callbacks only, the parent_feature() method returns the
parent of the current feature, if there is one. Called with a
numeric argument, ascends the parentage tree: parent_feature(1)
will return the parent, parent_feature(2) will return the
grandparent, etc. If there is no parent, returns undef.
$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
Bio::Graphics::Panel->add_track().
If the Bio::Graphics::Panel was initialized with -feature_limit set
to a non-zero value, then calls to a track glyph's add_feature()
method will maintain a count of features added to the track. Once
the feature count exceeds the value set in -feature_limit,
additional features will displace existing ones in a way that
effects a uniform sampling of the total feature set. This is useful
to protect against excessively large tracks. The total number of
features added can be retrieved by calling the glyph's
feature_count() method.
$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.
$subglyph = $glyph->make_subglyph($level,@sub_features)
This method is called to create subglyphs from a list of
subfeatures. The $level indicates the current level of the glyph
(top-level glyphs are level 0, subglyphs are level 1, etc).
Ordinarily this method simply calls
$self->factory->make_subglyph($level,@sub_features). Override it in
subclasses to create subglyphs of a particular type. For example:
sub make_subglyph {
my $self = shift;
my $level = shift;
my $factory = $self->factory;
$factory->make_glyph($factory,'arrow',@_);
}
$count = $glyph->feature_count()
Return the number of features added to this glyph via
add_feature().
$flag = $glyph->features_clipped()
If the panel was initialized with -feature_limit set to a non-zero
value, then calls to add_features() will limit the number of glyphs
to the indicated value. If this value was exceeded, then
features_clipped() will return true.
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 = $glyph->tkcolor
This method returns a color to be used to flood-fill the entire
glyph before drawing (currently used by the "track" glyph).
($left,$top,$right,$bottom) = $glyph->bounds($dx,$dy)
Given the topleft coordinates of the glyph, return the bounding box
of its contents, exclusive of padding. This is typically called by
the draw() and draw_component() methods to recover the position of
the glyph.
($left,$top,$right,$bottom) = $glyph->calculate_boundaries($dx,$dy)
An alias for bounds(), used by some glyphs for compatibility with
older versions of this module.
$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 = $glyph->color($option_name)
Given an option name that corresponds to a color (e.g. 'fgcolor')
look up the option and translate it into a GD color index.
$index = $glyph->translate_color($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.
@parts = $glyph->parts
For glyphs that can contain subparts (e.g. the segments glyph),
this method will return the list of subglyphs it contains.
Subglyphs are created automatically by the new() method and are
created subject to the maximum recursion depth specified by the
maxdepth() method and/or the -maxdepth option.
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 list of base position, given in base pair units, into
pixels, using the current scale and glyph position. This method
will accept a single base position or an array.
$glyph->filled_box($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.
Also try out the glyph_help.pl script, which attempts to document each
glyph's shared and specific options and provides an interface for
graphically inspecting the effect of different options.
Option Description Default
------------------------
-fgcolor Foreground color black
-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
-stranded Whether to indicate undef (false)
strandedness
(same as above))
-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">.
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 label. If you provide the numeric value "1" to -label,
the label 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. Multisegmented features will draw an arrowhead
on each component unless you specify a value of "ends" to
-strand_arrow, in which case only the rightmost component (for + strand
features) or the leftmost component (for - strand features) will have
arrowheads.
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). Finally, "name" will sort by the
display_name of the features.
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.
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.
SEE ALSO
Bio::DB::GFF::Feature, Ace::Sequence, Bio::Graphics::Panel,
Bio::Graphics::Track, Bio::Graphics::Glyph::Factory,
Bio::Graphics::Glyph::alignment, Bio::Graphics::Glyph::anchored_arrow,
Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::box,
Bio::Graphics::Glyph::broken_line, Bio::Graphics::Glyph::cds,
Bio::Graphics::Glyph::christmas_arrow, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::dashed_line, Bio::Graphics::Glyph::diamond,
Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot,
Bio::Graphics::Glyph::dumbbell, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::ex, Bio::Graphics::Glyph::extending_arrow,
Bio::Graphics::Glyph::flag, Bio::Graphics::Glyph::gene,
Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::group,
Bio::Graphics::Glyph::heterogeneous_segments,
Bio::Graphics::Glyph::image, Bio::Graphics::Glyph::lightning,
Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::merge_parts,
Bio::Graphics::Glyph::merged_alignment, Bio::Graphics::Glyph::minmax,
Bio::Graphics::Glyph::oval, Bio::Graphics::Glyph::pentagram,
Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::processed_transcript,
Bio::Graphics::Glyph::protein, Bio::Graphics::Glyph::ragged_ends,
Bio::Graphics::Glyph::redgreen_box,
Bio::Graphics::Glyph::redgreen_segment,
Bio::Graphics::Glyph::repeating_shape, Bio::Graphics::Glyph::rndrect,
Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::saw_teeth,
Bio::Graphics::Glyph::segmented_keyglyph,
Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::so_transcript,
Bio::Graphics::Glyph::span, Bio::Graphics::Glyph::splice_site,
Bio::Graphics::Glyph::stackedplot, Bio::Graphics::Glyph::ternary_plot,
Bio::Graphics::Glyph::text_in_box, Bio::Graphics::Glyph::three_letters,
Bio::Graphics::Glyph::tic_tac_toe, Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::track, Bio::Graphics::Glyph::transcript,
Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation,
Bio::Graphics::Glyph::triangle, Bio::Graphics::Glyph::two_bolts,
Bio::Graphics::Glyph::wave, Bio::Graphics::Glyph::weighted_arrow,
Bio::Graphics::Glyph::whiskerplot, Bio::Graphics::Glyph::xyplot
AUTHOR
Lincoln Stein <lstein@cshl.org>
Copyright (c) 2001 Cold Spring Harbor Laboratory
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.
perl v5.14.1 2011-07-22 Bio::Graphics::Glyph(3)
