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1 package Bio::Graphics::Glyph::splice_site;
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2
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3 use strict;
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4 use vars '@ISA';
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5 @ISA = 'Bio::Graphics::Glyph::generic';
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6 use Bio::Graphics::Glyph::generic;
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7
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8 use constant PWIDTH => 3;
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9
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10 sub draw_component {
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11 my $self = shift;
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12 my $gd = shift;
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13 my ($left,$top) = @_;
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14 my($x1,$y1,$x2,$y2) = $self->bounds(@_);
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15
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16 my $center = int(0.5+($x1+$x2)/2);
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17 my $direction = $self->option('direction');
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18
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19 my $height = $y2 - $y1;
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20 my $fraction = $self->option('height_fraction') || 1.0;
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21 my $bottom = $y2;
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22 $top = $y2 - $fraction * $height;
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23
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24 # draw the base
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25 my $fgcolor = $self->fgcolor;
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26 $gd->line($center,$bottom,$center,$top,$fgcolor);
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27
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28 if ($direction eq 'right') {
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29 $gd->line($center,$top,$center + PWIDTH,$top,$fgcolor);
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30 } elsif ($direction eq 'left') {
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31 $gd->line($center,$top,$center - PWIDTH,$top,$fgcolor);
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32 }
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33
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34 }
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35
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36 1;
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37
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38
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39 =head1 NAME
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40
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41 Bio::Graphics::Glyph::splice_site - The "splice_site" glyph
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42
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43 =head1 SYNOPSIS
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44
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45 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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46
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47 =head1 DESCRIPTION
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48
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49 This glyph was designed to show an inverted "L" representing splice
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50 donors and acceptors. The vertical part of the L points downwards and
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51 is positioned in the center of the range (even if the range is quite
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52 large).
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53
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54 In addition to the usual glyph options, this glyph recognizes:
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55
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56 Option Value Description
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57 ------ ----- -----------
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58
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59 direction "left" or "right" direction the short part of the L
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60 points
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61
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62 height_fraction 0.0 - 1.0 fractional height of the glyph,
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63 usually a callback that uses the
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64 feature's score to determine its
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65 height
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66
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67 =head1 BUGS
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68
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69 Please report them.
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70
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71 =head1 SEE ALSO
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72
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73
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74 L<Bio::Graphics::Panel>,
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75 L<Bio::Graphics::Glyph>,
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76 L<Bio::Graphics::Glyph::arrow>,
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77 L<Bio::Graphics::Glyph::cds>,
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78 L<Bio::Graphics::Glyph::crossbox>,
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79 L<Bio::Graphics::Glyph::diamond>,
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80 L<Bio::Graphics::Glyph::dna>,
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81 L<Bio::Graphics::Glyph::dot>,
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82 L<Bio::Graphics::Glyph::ellipse>,
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83 L<Bio::Graphics::Glyph::extending_arrow>,
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84 L<Bio::Graphics::Glyph::generic>,
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85 L<Bio::Graphics::Glyph::graded_segments>,
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86 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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87 L<Bio::Graphics::Glyph::line>,
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88 L<Bio::Graphics::Glyph::pinsertion>,
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89 L<Bio::Graphics::Glyph::primers>,
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90 L<Bio::Graphics::Glyph::rndrect>,
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91 L<Bio::Graphics::Glyph::chromosome>,
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92 L<Bio::Graphics::Glyph::segments>,
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93 L<Bio::Graphics::Glyph::ruler_arrow>,
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94 L<Bio::Graphics::Glyph::toomany>,
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95 L<Bio::Graphics::Glyph::transcript>,
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96 L<Bio::Graphics::Glyph::transcript2>,
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97 L<Bio::Graphics::Glyph::translation>,
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98 L<Bio::Graphics::Glyph::triangle>,
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99 L<Bio::DB::GFF>,
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100 L<Bio::SeqI>,
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101 L<Bio::SeqFeatureI>,
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102 L<Bio::Das>,
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103 L<GD>
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104
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105 =head1 AUTHOR
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106
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107 Xiaokang Pan E<lt>pan@cshl.orgE<gt>
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108
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109 Copyright (c) 2001 BDGP
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110
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111 This library is free software; you can redistribute it and/or modify
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112 it under the same terms as Perl itself. See DISCLAIMER.txt for
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113 disclaimers of warranty.
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114
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115 =cut
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