Raw content of Bio::Graphics::Glyph::Factory
<![CDATA[=head1 NAME
Bio::Graphics::Glyph::Factory - Factory for Bio::Graphics::Glyph objects
=head1 SYNOPSIS
See L<Bio::Graphics::Panel>.
=head1 DESCRIPTION
This class is used internally by Bio::Graphics to generate new Glyph
objects by combining a list of features with the user's desired
configuration. It is intended to be used internally by Bio::Graphics.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Lincoln Stein
Email - lstein@cshl.org
=head1 SEE ALSO
L<Bio::Graphics::Panel>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with an "_"
(underscore).
=cut
package Bio::Graphics::Glyph::Factory;
use strict;
use Carp qw(:DEFAULT cluck);
use GD;
my %LOADED_GLYPHS = ();
my %GENERIC_OPTIONS = (
bgcolor => 'turquoise',
fgcolor => 'black',
fontcolor => 'black',
font2color => 'turquoise',
height => 8,
font => gdSmallFont,
bump => +1, # bump by default (perhaps a mistake?)
);
=head2 new
Title : new
Usage : $f = Bio::Graphics::Glyph::Factory->new(
-stylesheet => $stylesheet,
-glyph_map => $glyph_map,
-options => $options);
Function : create a new Bio::Graphics::Glyph::Factory object
Returns : the new object
Args : $stylesheet is a Bio::Das::Stylesheet object that can
convert Bio::Das feature objects into glyph names and
associated options.
$glyph_map is a hash that maps primary tags to glyph names.
$options is a hash that maps option names to their values.
Status : Internal to Bio::Graphics
=cut
sub new {
my $class = shift;
my $panel = shift;
my %args = @_;
my $stylesheet = $args{-stylesheet}; # optional, for Bio::Das compatibility
my $map = $args{-map}; # map type name to glyph name
my $options = $args{-options}; # map type name to glyph options
return bless {
stylesheet => $stylesheet,
glyph_map => $map,
options => $options,
panel => $panel,
},$class;
}
=head2 clone
Title : clone
Usage : $f2 = $f->clone
Function : Deep copy of a factory object
Returns : a deep copy of the factory object
Args : None
Status : Internal to Bio::Graphics
=cut
sub clone {
my $self = shift;
my %new = %$self;
my $new = bless \%new,ref($self);
$new;
}
=head2 stylesheet
Title : stylesheet
Usage : $stylesheet = $f->stylesheet
Function : accessor for stylesheet
Returns : a Bio::Das::Stylesheet object
Args : None
Status : Internal to Bio::Graphics
=cut
sub stylesheet { shift->{stylesheet} }
=head2 glyph_map
Title : glyph_map
Usage : $map = $f->glyph_map
Function : accessor for the glyph map
Returns : a hash mapping primary tags to glyphs
Args : None
Status : Internal to Bio::Graphics
=cut
sub glyph_map { shift->{glyph_map} }
=head2 option_map
Title : option_map
Usage : $map = $f->option_map
Function : accessor for the option map
Returns : a hash mapping option names to values
Args : None
Status : Internal to Bio::Graphics
=cut
sub option_map { shift->{options} }
=head2 global_opts
Title : global_opts
Usage : $map = $f->global_opts
Function : accessor for global options
Returns : a hash mapping option names to values
Args : None
Status : Internal to Bio::Graphics
This returns a set of defaults for option values.
=cut
sub global_opts{ shift->{global_opts} }
=head2 panel
Title : panel
Usage : $panel = $f->panel
Function : accessor for Bio::Graphics::Panel
Returns : a Bio::Graphics::Panel
Args : None
Status : Internal to Bio::Graphics
This returns the panel with which the factory is associated.
=cut
sub panel { shift->{panel} }
=head2 scale
Title : scale
Usage : $scale = $f->scale
Function : accessor for the scale
Returns : a floating point number
Args : None
Status : Internal to Bio::Graphics
This returns the scale, in pixels/bp for glyphs constructed by this
factory.
=cut
sub scale { shift->{panel}->scale }
=head2 font
Title : font
Usage : $font = $f->font
Function : accessor for the font
Returns : a font name
Args : None
Status : Internal to Bio::Graphics
This returns a GD font name.
=cut
sub font {
my $self = shift;
my $glyph = shift;
$self->option($glyph,'font') || $self->{font};
}
=head2 map_pt
Title : map_pt
Usage : @pixel_positions = $f->map_pt(@bp_positions)
Function : map bp positions to pixel positions
Returns : a list of pixel positions
Args : a list of bp positions
Status : Internal to Bio::Graphics
The real work is done by the panel, but factory subclasses can
override if desired.
=cut
sub map_pt {
my $self = shift;
my @result = $self->panel->map_pt(@_);
return wantarray ? @result : $result[0];
}
=head2 map_no_trunc
Title : map_no_trunc
Usage : @pixel_positions = $f->map_no_trunc(@bp_positions)
Function : map bp positions to pixel positions
Returns : a list of pixel positions
Args : a list of bp positions
Status : Internal to Bio::Graphics
Same as map_pt(), but it will NOT clip pixel positions to be within
the drawing frame.
=cut
sub map_no_trunc {
my $self = shift;
my @result = $self->panel->map_no_trunc(@_);
return wantarray ? @result : $result[0];
}
=head2 translate_color
Title : translate_color
Usage : $index = $f->translate_color($color_name)
Function : translate symbolic color names into GD indexes
Returns : an integer
Args : a color name in format "green" or "#00FF00"
Status : Internal to Bio::Graphics
The real work is done by the panel, but factory subclasses can
override if desired.
=cut
sub translate_color {
my $self = shift;
my $color_name = shift;
$self->panel->translate_color($color_name);
}
=head2 glyph
Title : glyph
Usage : @glyphs = $f->glyph($level,$feature1,$feature2...)
Function : transform features into glyphs.
Returns : a list of Bio::Graphics::Glyph objects
Args : a feature "level", followed by a list of FeatureI objects.
Status : Internal to Bio::Graphics
The level is used to track the level of nesting of features that have
subfeatures.
=cut
# create a glyph
sub make_glyph {
my $self = shift;
my $level = shift;
my @result;
my $panel = $self->panel;
my ($leftmost,$rightmost) = ($panel->left,$panel->right);
my $flip = $panel->flip;
for my $f (@_) {
my $type = $self->feature_to_glyph($f);
my $glyphclass = 'Bio::Graphics::Glyph';
$type ||= 'generic';
$glyphclass .= "\:\:\L$type";
unless ($LOADED_GLYPHS{$glyphclass}++) {
carp("the requested glyph class, ``$type'' is not available: $@")
unless (eval "require $glyphclass");
}
my $glyph = $glyphclass->new(-feature => $f,
-factory => $self,
-flip => $flip,
-level => $level);
# this is removing glyphs that are not onscreen at all.
# But never remove tracks!
push @result,$glyph if $type eq 'track'
|| ($glyph->{left} + $glyph->{width} > $leftmost && $glyph->{left} < $rightmost);
}
return wantarray ? @result : $result[0];
}
=head2 feature_to_glyph
Title : feature_to_glyph
Usage : $glyph_name = $f->feature_to_glyph($feature)
Function : choose the glyph name given a feature
Returns : a glyph name
Args : a Bio::Seq::FeatureI object
Status : Internal to Bio::Graphics
=cut
sub feature_to_glyph {
my $self = shift;
my $feature = shift;
return scalar $self->{stylesheet}->glyph($feature) if $self->{stylesheet};
my $map = $self->glyph_map or return 'generic';
if (ref($map) eq 'CODE') {
my $val = eval {$map->($feature)};
warn $@ if $@;
return $val || 'generic';
}
return $map->{$feature->primary_tag} || 'generic';
}
=head2 set_option
Title : set_option
Usage : $f->set_option($option_name=>$option_value)
Function : set or change an option
Returns : nothing
Args : a name/value pair
Status : Internal to Bio::Graphics
=cut
sub set_option {
my $self = shift;
my ($option_name,$option_value) = @_;
$self->{overriding_options}{lc $option_name} = $option_value;
}
# options:
# the overriding_options hash has precedence
# ...followed by the option_map
# ...followed by the stylesheet
# ...followed by generic options
sub option {
my $self = shift;
my ($glyph,$option_name,$partno,$total_parts) = @_;
return unless defined $option_name;
$option_name = lc $option_name; # canonicalize
return $self->{overriding_options}{$option_name}
if exists $self->{overriding_options} && exists $self->{overriding_options}{$option_name};
if (my $map = $self->option_map) {
if (defined(my $value = $map->{$option_name})) {
my $feature = $glyph->feature;
return $value unless ref $value eq 'CODE';
return unless $feature->isa('Bio::SeqFeatureI');
my $val = eval { $value->($feature,$option_name,$partno,$total_parts,$glyph)};
warn $@ if $@;
return defined $val && $val eq '*default*' ? $GENERIC_OPTIONS{$option_name} : $val;
}
}
if (my $ss = $self->stylesheet) {
my($glyph,%options) = $ss->glyph($glyph->feature);
my $value = $options{$option_name};
return $value if defined $value;
}
return $GENERIC_OPTIONS{$option_name};
}
=head2 options
Title : options
Usage : @option_names = $f->options
Function : return all configured option names
Returns : a list of option names
Args : none
Status : Internal to Bio::Graphics
=cut
# return names of all the options in the option hashes
sub options {
my $self = shift;
my %options;
if (my $map = $self->option_map) {
$options{lc($_)}++ foreach keys %$map;
}
$options{lc($_)}++ foreach keys %GENERIC_OPTIONS;
return keys %options;
}
1;
]]>