|
0
|
1 package Bio::Graphics::Glyph::alignment;
|
|
|
2
|
|
|
3 use strict;
|
|
|
4
|
|
|
5 use Bio::Graphics::Glyph::graded_segments;
|
|
|
6 use vars '@ISA';
|
|
|
7 @ISA = 'Bio::Graphics::Glyph::graded_segments';
|
|
|
8
|
|
|
9 1;
|
|
|
10
|
|
|
11 __END__
|
|
|
12
|
|
|
13 =head1 NAME
|
|
|
14
|
|
|
15 Bio::Graphics::Glyph::alignment - The "alignment" glyph
|
|
|
16
|
|
|
17 =head1 SYNOPSIS
|
|
|
18
|
|
|
19 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
|
|
|
20
|
|
|
21 =head1 DESCRIPTION
|
|
|
22
|
|
|
23 This is identical to the "graded_segments" glyph, and is used for
|
|
|
24 drawing features that consist of discontinuous segments. The
|
|
|
25 color intensity of each segment is proportionate to the score.
|
|
|
26
|
|
|
27 =head2 OPTIONS
|
|
|
28
|
|
|
29 The following options are standard among all Glyphs. See
|
|
|
30 L<Bio::Graphics::Glyph> for a full explanation.
|
|
|
31
|
|
|
32 Option Description Default
|
|
|
33 ------ ----------- -------
|
|
|
34
|
|
|
35 -fgcolor Foreground color black
|
|
|
36
|
|
|
37 -outlinecolor Synonym for -fgcolor
|
|
|
38
|
|
|
39 -bgcolor Background color turquoise
|
|
|
40
|
|
|
41 -fillcolor Synonym for -bgcolor
|
|
|
42
|
|
|
43 -linewidth Line width 1
|
|
|
44
|
|
|
45 -height Height of glyph 10
|
|
|
46
|
|
|
47 -font Glyph font gdSmallFont
|
|
|
48
|
|
|
49 -connector Connector type 0 (false)
|
|
|
50
|
|
|
51 -connector_color
|
|
|
52 Connector color black
|
|
|
53
|
|
|
54 -label Whether to draw a label 0 (false)
|
|
|
55
|
|
|
56 -description Whether to draw a description 0 (false)
|
|
|
57
|
|
|
58 -strand_arrow Whether to indicate 0 (false)
|
|
|
59 strandedness
|
|
|
60
|
|
|
61
|
|
|
62 In addition, the alignment glyph recognizes the following
|
|
|
63 glyph-specific options:
|
|
|
64
|
|
|
65 Option Description Default
|
|
|
66 ------ ----------- -------
|
|
|
67
|
|
|
68 -max_score Maximum value of the Calculated
|
|
|
69 feature's "score" attribute
|
|
|
70
|
|
|
71 -min_score Minimum value of the Calculated
|
|
|
72 feature's "score" attribute
|
|
|
73
|
|
|
74 If max_score and min_score are not specified, then the glyph will
|
|
|
75 calculate the local maximum and minimum scores at run time.
|
|
|
76
|
|
|
77
|
|
|
78 =head1 BUGS
|
|
|
79
|
|
|
80 Please report them.
|
|
|
81
|
|
|
82 =head1 SEE ALSO
|
|
|
83
|
|
|
84 L<Bio::Graphics::Panel>,
|
|
|
85 L<Bio::Graphics::Glyph>,
|
|
|
86 L<Bio::Graphics::Glyph::arrow>,
|
|
|
87 L<Bio::Graphics::Glyph::cds>,
|
|
|
88 L<Bio::Graphics::Glyph::crossbox>,
|
|
|
89 L<Bio::Graphics::Glyph::diamond>,
|
|
|
90 L<Bio::Graphics::Glyph::dna>,
|
|
|
91 L<Bio::Graphics::Glyph::dot>,
|
|
|
92 L<Bio::Graphics::Glyph::ellipse>,
|
|
|
93 L<Bio::Graphics::Glyph::extending_arrow>,
|
|
|
94 L<Bio::Graphics::Glyph::generic>,
|
|
|
95 L<Bio::Graphics::Glyph::graded_segments>,
|
|
|
96 L<Bio::Graphics::Glyph::heterogeneous_segments>,
|
|
|
97 L<Bio::Graphics::Glyph::line>,
|
|
|
98 L<Bio::Graphics::Glyph::pinsertion>,
|
|
|
99 L<Bio::Graphics::Glyph::primers>,
|
|
|
100 L<Bio::Graphics::Glyph::rndrect>,
|
|
|
101 L<Bio::Graphics::Glyph::segments>,
|
|
|
102 L<Bio::Graphics::Glyph::ruler_arrow>,
|
|
|
103 L<Bio::Graphics::Glyph::toomany>,
|
|
|
104 L<Bio::Graphics::Glyph::transcript>,
|
|
|
105 L<Bio::Graphics::Glyph::transcript2>,
|
|
|
106 L<Bio::Graphics::Glyph::translation>,
|
|
|
107 L<Bio::Graphics::Glyph::triangle>,
|
|
|
108 L<Bio::DB::GFF>,
|
|
|
109 L<Bio::SeqI>,
|
|
|
110 L<Bio::SeqFeatureI>,
|
|
|
111 L<Bio::Das>,
|
|
|
112 L<GD>
|
|
|
113
|
|
|
114 =head1 AUTHOR
|
|
|
115
|
|
|
116 Allen Day E<lt>day@cshl.orgE<gt>.
|
|
|
117
|
|
|
118 Copyright (c) 2001 Cold Spring Harbor Laboratory
|
|
|
119
|
|
|
120 This library is free software; you can redistribute it and/or modify
|
|
|
121 it under the same terms as Perl itself. See DISCLAIMER.txt for
|
|
|
122 disclaimers of warranty.
|
|
|
123
|
|
|
124 =cut
|
