Bio::Graphics::Glyph::line - The "line" glyph


Bio-Graphics documentation Contained in the Bio-Graphics distribution.

Index


Code Index:

NAME

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Bio::Graphics::Glyph::line - The "line" glyph

SYNOPSIS

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  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

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This glyph draws a line parallel to the sequence segment. It is different from other glyphs in that it is designed to work with DAS tracks. The line is drawn BETWEEN the subparts, as if you specified a connector type of "line".

OPTIONS

This glyph takes only the standard options. See 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)

BUGS

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Please report them.

SEE ALSO

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Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD

AUTHOR

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Allen Day <day@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.


Bio-Graphics documentation Contained in the Bio-Graphics distribution.

package Bio::Graphics::Glyph::line;
# $Id: line.pm,v 1.3 2009-06-04 21:51:08 lstein Exp $

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

sub my_description {
    return <<END;
This glyph draws a horizontal line spanning the feature.
END
}

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

    my $gd = shift;

    my $fg = $self->fgcolor;
    my $linewidth = $self->linewidth;
    $fg = $self->set_pen($linewidth) if $linewidth > 1;

    my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);
    my $center = ($y1+$y2)/2;

    my ($lowest,$highest);

    my @parts = $self->parts;
    my $previous = -1;
    for (my $i = 0;$i<@parts;$i++) {
	my $part      = $parts[$i];
	my ($l,undef,$xx1,$yy1) = $part->calculate_boundaries(@_);

	$lowest  = $l   if !defined $lowest  || $lowest > $l;
	$highest = $xx1 if !defined $xx1     || $highest < $xx1;

	my $next_part = $parts[$i+1] or last;
	my ($xx2,$yy2,undef,undef) = $next_part->calculate_boundaries(@_);

	$self->draw_connector($gd,$xx1,$xx2,$y1,$y2) if $xx1 < $xx2;
    }

    if ($lowest && $x1 < $lowest) {
	$self->draw_connector($gd,$x1,$lowest,$y1,$y2);
    }

    if ($highest && $x2 > $highest) {
	$self->draw_connector($gd,$highest,$x2,$y1,$y2);
    }

    my $height = $self->height;
    $height    = 12 unless $height > 12;

    return unless $self->parts;
    if ($self->feature->strand > 0) {
	$self->arrow($gd,$x2,$x2+$height/2,$center);
    } elsif ($self->feature->strand < 0) {
	$self->arrow($gd,$x1,$x1-$height/2,$center);
    }
}

sub draw_connector {
    my $self = shift;
    my $gd   = shift;
    my ($left,$right,$high,$low) = @_;
    my $fg = $self->fgcolor;
    my $center = ($high+$low)/2;
    $gd->line($left,$center,$right,$center,$fg);
}

sub bump { 0 }

sub maxdepth { return }


1;

__END__