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package Bio::Graphics::Glyph::transcript2;
use strict;
use base qw(Bio::Graphics::Glyph::transcript);
use constant MIN_WIDTH_FOR_ARROW => 8;
sub show_strand {
my $self = shift;
my $s = $self->SUPER::show_strand;
return $s if defined $s;
return 'ends';
}
sub extra_arrow_length {
my $self = shift;
my $strand = $self->feature->strand || 0;
$strand *= -1 if $self->{flip};
my $first = $strand < 0 ? ($self->parts)[0]
: ($self->parts)[-1];
$first ||= $self;
my @rect = $first->bounds();
my $width = abs($rect[2] - $rect[0]);
return 0 if $width >= MIN_WIDTH_FOR_ARROW;
return $self->arrow_length;
}
sub pad_left {
my $self = shift;
my $pad = $self->Bio::Graphics::Glyph::generic::pad_left;
return $pad if $self->feature->strand > 0;
my $extra_arrow_length = $self->extra_arrow_length;
if ($self->label_position eq 'left' && $self->label) {
return $extra_arrow_length+$pad;
} else {
return $extra_arrow_length > $pad ? $extra_arrow_length : $pad;
}
}
sub pad_right {
my $self = shift;
my $pad = $self->Bio::Graphics::Glyph::generic::pad_right;
return $pad if $self->feature->strand < 0;
my $extra_arrow_length = $self->extra_arrow_length;
return $extra_arrow_length > $pad ? $extra_arrow_length : $pad;
}
sub draw_connectors {
my $self = shift;
my ($gd,$dx,$dy) = @_;
my $part;
my $strand = $self->feature->strand;
$strand *= -1 if $self->{flip}; #sigh
if (my @parts = $self->parts) {
$part = $strand >= 0 ? $parts[-1] : $parts[0];
} elsif ($self->feature_has_subparts) {
# no parts -- so draw an intron spanning whole thing
my($x1,$y1,$x2,$y2) = $self->bounds(0,0);
$self->_connector($gd,$dx,$dy,$x1,$y1,$x1,$y2,$x2,$y1,$x2,$y2);
$part = $self;
} else {
return;
}
my @rect = $part->bounds();
my $width = abs($rect[2] - $rect[0]);
my $filled = $width >= MIN_WIDTH_FOR_ARROW;
if ($filled) {
$self->Bio::Graphics::Glyph::generic::draw_connectors(@_);
} else {
$self->SUPER::draw_connectors(@_);
}
}
sub draw_component {
my $self = shift;
return unless $self->level > 0;
my $gd = shift;
my ($left,$top) = @_;
my @rect = $self->bounds(@_);
my $f = $self->feature;
my $strand = $f->strand;
my $str = $strand * ($self->{flip} ? -1 : 1);
my $width = abs($rect[2] - $rect[0]);
my $filled = defined($self->{partno}) && $width >= MIN_WIDTH_FOR_ARROW;
my ($pwidth) = $gd->getBounds;
$filled = 0 if $str < 0 && $rect[0] < $self->panel->pad_left;
$filled = 0 if $str > 0 && $rect[2] > $pwidth - $self->panel->pad_right;
if ($self->stranded && $filled) {
my ($first,$last) = ($self->{partno} == 0 , $self->{partno} == $self->{total_parts}-1);
($first,$last) = ($last,$first) if $self->{flip};
if ($strand < 0 && $first) { # first exon, minus strand transcript
$self->filled_arrow($gd,-1,@rect);
} elsif ($strand >= 0 && $last) { # last exon, plus strand
$self->filled_arrow($gd,+1,@rect);
} else {
$self->filled_box($gd,@rect);
}
}
else {
$self->filled_box($gd,@rect);
}
# copied from generic::draw_component
$self->draw_translation($gd,@_) if $self->{cds_translation}; # created earlier by calculate_cds()
$self->draw_sequence($gd,@_) if $self->option('draw_dna') && $self->dna_fits;
}
sub bump {
my $self = shift;
return $self->SUPER::bump(@_) if $self->all_callbacks;
return 0; # never allow our components to bump
}
1;
__END__
=head1 NAME
Bio::Graphics::Glyph::transcript2 - The "transcript2" glyph
=head1 SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 DESCRIPTION
This glyph is used for drawing transcripts. It is like "transcript"
except that if there is sufficient room the terminal exon is shaped
like an arrow in order to indicate the direction of transcription. If
there isn't enough room, a small arrow is drawn.
=head2 OPTIONS
The following options are standard among all Glyphs. See
L<Bio::Graphics::Glyph> for a full explanation.
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 0 (false)
-connector_color
Connector color black
-label Whether to draw a label 0 (false)
-description Whether to draw a description 0 (false)
-strand_arrow Whether to indicate 0 (false)
strandedness
-hilite Highlight color undef (no color)
In addition, the alignment glyph recognizes the following
glyph-specific options:
Option Description Default
------ ----------- -------
-arrow_length Length of the directional 8
arrow.
=head1 BUGS
Please report them.
=head1 SEE ALSO
L<Bio::Graphics::Panel>,
L<Bio::Graphics::Glyph>,
L<Bio::Graphics::Glyph::arrow>,
L<Bio::Graphics::Glyph::cds>,
L<Bio::Graphics::Glyph::crossbox>,
L<Bio::Graphics::Glyph::diamond>,
L<Bio::Graphics::Glyph::dna>,
L<Bio::Graphics::Glyph::dot>,
L<Bio::Graphics::Glyph::ellipse>,
L<Bio::Graphics::Glyph::extending_arrow>,
L<Bio::Graphics::Glyph::generic>,
L<Bio::Graphics::Glyph::graded_segments>,
L<Bio::Graphics::Glyph::heterogeneous_segments>,
L<Bio::Graphics::Glyph::line>,
L<Bio::Graphics::Glyph::pinsertion>,
L<Bio::Graphics::Glyph::primers>,
L<Bio::Graphics::Glyph::rndrect>,
L<Bio::Graphics::Glyph::segments>,
L<Bio::Graphics::Glyph::ruler_arrow>,
L<Bio::Graphics::Glyph::toomany>,
L<Bio::Graphics::Glyph::transcript>,
L<Bio::Graphics::Glyph::transcript2>,
L<Bio::Graphics::Glyph::translation>,
L<Bio::Graphics::Glyph::triangle>,
L<Bio::DB::GFF>,
L<Bio::SeqI>,
L<Bio::SeqFeatureI>,
L<Bio::Das>,
L<GD>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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.
=cut
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