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package Bio::Graphics::Glyph::read_pair;
#specialized for SAM read pairs
use base 'Bio::Graphics::Glyph::segments';
sub my_description {
return <<END;
This glyph is designed to be used with SAM/BAM paired end read/mate-pair data. It has
the same properties as the segments glyph, but draws mate pairs as two gapped alignments
connected by dashed lines. Mate pairs that overlap are rendered in a rational fashion.
END
}
sub connector {
my $self = shift;
return $self->level == 0 ? 'dashed' : 'solid';
}
sub parts_overlap { 1 }
sub box_subparts { 2 }
sub stranded {
my $self = shift;
my $s = $self->SUPER::stranded;
return defined $s ? $s : 1;
}
sub bgcolor {
my $self = shift;
my $bg = $self->option('bgcolor');
$bg = $self->feature->strand > 0 ? 'red' : 'blue' unless defined $bg;
return $self->factory->translate_color($bg);
}
sub draw_target {
my $self = shift;
my $t = $self->option('draw_target');
return $t if defined $t;
return 1;
}
sub show_mismatch {
my $self = shift;
my $t = $self->option('show_mismatch');
return $t if defined $t;
return 1;
}
sub label_position {
my $self = shift;
my $t = $self->option('label_position');
return $t if defined $t;
return 'left';
}
sub maxdepth { 2 }
1;
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