Bio::Graphics::Glyph ruler_arrow
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Summary
Bio::Graphics::Glyph::arrow - The "ruler_arrow" glyph
Package variables
Privates (from "my" definitions)
%UNITS = (K => 1000, M => 1_000_000, G => 1_000_000_000)
Included modules
Bio::Graphics::Glyph::generic
Inherit
Bio::Graphics::Glyph::generic
Synopsis
  See Bio::Graphics::Panel and Bio::Graphics::Glyph.
Description
This glyph draws arrows. Label, if requested, will be 5' and 3' at both ends
and tick scale is printed if no_tick_label option is set and tick option set.
Depending on options, the arrows can be labeled, be oriented vertically
or horizontally, or can contain major and minor ticks suitable for use as a scale. In addition to the common options, the following glyph-specific
options are recognized:
  Option      Description               Default
------ ----------- -------
-tick Whether to draw major 0 and minor ticks. 0 = no ticks 1 = major ticks 2 = minor ticks -label 5' at start, 3' at end 0 above arrow -both 5', 3' above, 0 and 3', 5' below arrow -direction 0 = ruler is plus strand 0 -1 = ruler is minus strand -parallel Whether to draw the arrow true parallel to the sequence or perpendicular to it. -northeast Force a north or east true arrowhead(depending on orientation) -east synonym of above -southwest Force a south or west true arrowhead(depending on orientation) -west synonym of above -double force-doubleheaded arrow -base Draw a vertical base at the false non-arrowhead side -scale Reset the labels on the arrow false to reflect an externally established scale.
Set -parallel to false to display a point-like feature such as a
polymorphism, or to indicate an important location. If the feature
start == end, then the glyph will draw a single arrow at the
designated location:
       ^
|
Otherwise, there will be two arrows at the start and end:
       ^              ^
| |
Scale: Pass in a externally established scale to reset the labels on
the arrow. This is particularly useful for manually constructed
images where the founding parameters of the panel are not 1-based.
For example, a genetic map interval ranging from 0.1 - 0.3 can be
constructed by first multiplying every value by 100. Passing
  arrow(-scale=>100);
will draw tick marks labelled appropriately to your external scale.
Methods
arrowheads
No description
Code
draw
No description
Code
draw_label
No description
Code
draw_parallel
No description
Code
draw_perpendicular
No description
Code
pad_bottom
No description
Code
Methods description
None available.
Methods code
arrowheadsdescriptionprevnextTop
sub arrowheads {
  my $self = shift;
  my ($ne,$sw,$base_e,$base_w);
  if ($self->option('double')) {
    $ne = $sw = 1;
  } else {
    $ne   = $self->option('northeast') || $self->option('east');
    $sw   = $self->option('southwest') || $self->option('west');
  }
  # otherwise use strandedness to define the arrow
unless (defined($ne) || defined($sw)) { # turn on both if neither specified
$ne = 1 if $self->feature->strand > 0; $sw = 1 if $self->feature->strand < 0; } return ($sw,$ne,0,0) unless $self->option('base'); return ($sw,$ne,!$sw,!$ne);
}
drawdescriptionprevnextTop
sub draw {
  my $self = shift;
  my $parallel = $self->option('parallel');
  $parallel = 1 unless defined $parallel;
  $self->draw_parallel(@_) if $parallel;
  $self->draw_perpendicular(@_) unless $parallel;
  $self->draw_label(@_) if ($self->option('label'));
}
draw_labeldescriptionprevnextTop
sub draw_label {
  my $self = shift;
  my ($gd,$left,$top) = @_;

  my $label5 = "5'";
  my $label3 = "3'";
  my $relative = $self->option('relative_coords');
  my $start    = $relative ? 1 : $self->feature->start;
  my $stop     = $start + $self->feature->length  - 1;

  my $offset   = $relative ? $self->feature->start-1 : 0;
  my $reversed = $self->feature->strand < 0;

  my $units = $self->option('units') || '';
  my $divisor = $UNITS{$units} || 1 if $units;

  my ($major_ticks,$minor_ticks) = $self->panel->ticks($start,$stop,$self->font,$divisor);
  my $tick_scale = " ($major_ticks bp/";
  $tick_scale .= ($self->option('tick') >= 2)?"major tick)":"tick)";

  my $top_left_label = $label5;
  $top_left_label .= $tick_scale if ($self->option('no_tick_label') && $self->option('tick'));
  #-1 direction mean lower end is 3' (minus strand on top)
($label5, $label3) = ($label3, $label5) if ($self->option('direction') == -1); my $x = $self->left + $left; $x = $self->panel->left + 1 if $x <= $self->panel->left; my $font = $self->option('labelfont') || $self->font; $gd->string($font, $x, $self->top + $top, $top_left_label, $self->fontcolor); my $x1 = $left + $self->panel->right - $font->width*length($label3); $gd->string($font, $x1, $self->top + $top, $label3, $self->fontcolor); if ($self->option('both')) {#minus strand as well
$gd->string($font, $x, $self->bottom - $self->pad_bottom + $top, $label3, $self->fontcolor); my $x1 = $left + $self->panel->right - $font->width*length($label5); $gd->string($font, $x1, $self->bottom - $self->pad_bottom + $top, $label5, $self->fontcolor); } } 1; __END__
}
draw_paralleldescriptionprevnextTop
sub draw_parallel {
  my $self = shift;
  my $gd = shift;
  my ($dx,$dy) = @_;
  my ($x1,$y1,$x2,$y2) = $self->bounds(@_);

  my $fg = $self->set_pen;
  my $a2 = ($self->height)/2;
my $center = $y1+$a2; $x1 = $self->panel->left if $x1 < $self->panel->left; $x2 = $self->panel->right if $x2 > $self->panel->right; my ($sw,$ne,$base_w,$base_e) = $self->arrowheads; $gd->line($x1,$center,$x2,$center,$fg); $self->arrowhead($gd,$x1,$center,$a2,-1) if $sw; # west arrow
$self->arrowhead($gd,$x2,$center,$a2,+1) if $ne; # east arrow
$gd->line($x2,$center-$a2,$x2,$center+$a2,$fg) if $base_e; #east base
$gd->line($x1,$center-$a2,$x1,$center+$a2,$fg) if $base_w; #west base
# turn on ticks
if ($self->option('tick')) { local $^W = 0; # dumb uninitialized variable warning
my $font = $self->font; my $width = $font->width; my $font_color = $self->fontcolor; my $height = $self->height; my $relative = $self->option('relative_coords'); my $start = $relative ? 1 : $self->feature->start; my $stop = $start + $self->feature->length - 1; my $offset = $relative ? $self->feature->start-1 : 0; my $reversed = $self->feature->strand < 0; my $units = $self->option('units') || ''; my $divisor = $UNITS{$units} || 1 if $units; my ($major_ticks,$minor_ticks) = $self->panel->ticks($start,$stop,$font,$divisor); ## Does the user want to override the internal scale?
my $scale = $self->option('scale'); my $left = $sw ? $x1+$height : $x1; my $right = $ne ? $x2-$height : $x2; my $format = ($major_ticks->[1]-$major_ticks->[0])/($divisor||1) < 1 ? "%.1f$units" : "%d$units";
for my $i (@$major_ticks) { my $tickpos = $dx + ($reversed ? $self->map_pt($stop - $i + $offset) : $self->map_pt($i + $offset)); next if $tickpos < $left or $tickpos > $right; $gd->line($tickpos,$center-$a2,$tickpos,$center+$a2,$fg); my $label = $scale ? $i / $scale : $i;
if ($units) { my $scaled = $label/$divisor;
$label = sprintf($format,$scaled); } my $middle = $tickpos - (length($label) * $width)/2;
$gd->string($font,$middle,$center+$a2-1,$label,$font_color) unless ($self->option('no_tick_label')); } if ($self->option('tick') >= 2) { my $a4 = $self->height/4;
for my $i (@$minor_ticks) { my $tickpos = $dx + ($reversed ? $self->map_pt($stop - $i + $offset) : $self->map_pt($i + $offset)); next if $tickpos < $left or $tickpos > $right; $gd->line($tickpos,$center-$a4,$tickpos,$center+$a4,$fg); } } } # add a label if requested
# $self->draw_label($gd,$dx,$dy) if ($self->option('label');
# $self->draw_description($gd,$dx,$dy) if $self->option('description');
}
draw_perpendiculardescriptionprevnextTop
sub draw_perpendicular {
  my $self = shift;
  my $gd = shift;
  my ($dx,$dy) = @_;
  my ($x1,$y1,$x2,$y2) = $self->bounds(@_);

  my $ne = $self->option('northeast');
  my $sw = $self->option('southwest');
  $ne = $sw = 1 unless defined($ne) || defined($sw);

  # draw a perpendicular arrow at position indicated by $x1
my $fg = $self->set_pen; my $a2 = ($y2-$y1)/4;
my @positions = $x1 == $x2 ? ($x1) : ($x1,$x2); for my $x (@positions) { if ($ne) { $gd->line($x,$y1,$x,$y2,$fg); $gd->line($x-$a2,$y1+$a2,$x,$y1,$fg); $gd->line($x+$a2,$y1+$a2,$x,$y1,$fg); } if ($sw) { $gd->line($x,$y1,$x,$y2,$fg); $gd->line($x-$a2,$y2-$a2,$x,$y2,$fg); $gd->line($x+$a2,$y2-$a2,$x,$y2,$fg); } } # add a label if requested
# $self->draw_label($gd,$dx,$dy) if ($self->option('label') && !$self->option('ruler'));
# this draws the label aligned to the left
}
pad_bottomdescriptionprevnextTop
sub pad_bottom {
  my $self = shift;
  my $val = $self->SUPER::pad_bottom(@_);
  $val += $self->font->height if $self->option('tick');
  $val;
}

# override draw method
}
General documentation
BUGSTop
Please report them.
SEE ALSOTop
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
AUTHORTop
Shengqiang Shu <sshu@bdgp.lbl.gov>
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 BDGP, 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.