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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Graphics::Glyph::image \- A glyph that draws photographs & other images .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 3 \& use Bio::Graphics; \& use Bio::Seq; \& use Bio::SeqFeature::Generic; \& \& my $bsg = \*(AqBio::SeqFeature::Generic\*(Aq; \& \& my $seq = Bio::Seq\->new(\-length=>1000); \& \& my $whole = $bsg\->new(\-display_name => \*(AqClone82\*(Aq, \& \-start => 1, \& \-end => $seq\->length); \& \& my $image1 = $bsg\->new(\-start => 100, \& \-end => 300, \& \-display_name => \*(AqExcretory System\*(Aq, \& \-tag=>{ \& image=>"http://www.flybase.org/anatomy/image\-browser_files/excretory\-system.gif" \& } \& ); \& \& my $image2 = $bsg\->new(\-start => 500, \& \-end => 800, \& \-display_name => \*(AqExpression Pattern\*(Aq, \& \-tag=>{ \& image=>"http://www.flybase.org/anatomy/image\-browser_files/embryonic\-expression\-pattern.gif" \& } \& ); \& \& my $panel = Bio::Graphics::Panel\->new(\-length => $seq\->length, \& \-width => 800, \& \-truecolor => 1, \& \-key_style => \*(Aqbetween\*(Aq, \& \-pad_left => 10, \& \-pad_right => 10, \& ); \& \& $panel\->add_track($whole, \& \-glyph => \*(Aqarrow\*(Aq, \& \-double => 1, \& \-tick => 2, \& \-label => 1, \& ); \& \& $panel\->add_track([$image1,$image2], \& \-glyph => \*(Aqimage\*(Aq, \& \-label => 1, \& \-key => \*(AqExample images\*(Aq); \& \& binmode STDOUT; \& print $panel\->png; .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This glyph inserts an image into the track at the indicated feature coordinates. The image can be in \s-1PNG, JPEG, GIF\s0 or \s-1GD\s0 format, and can be either 8\-bit or 24\-bit (\*(L"truecolor\*(R"). The image can be located on the local filesystem or located at a remote \s-1URL\s0 (provided that you have the \s-1LWP\s0 module installed). .PP When working with photographic images, you may wish to have Bio::Graphics::Panel create 24\-bit (truecolor) images in order to avoid running out of colors. The symptom of this is that images appear posterized. To turn on truecolor images, pass the \-truecolor option to Bio::Graphics::Panel as shown in the synopsis. .SS "\s-1OPTIONS\s0" .IX Subsection "OPTIONS" The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation. .PP .Vb 2 \& 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) \& \& \-hilite Highlight color undef (no color) .Ve .PP The following additional options are available to the \*(L"image\*(R" glyph: .PP .Vb 2 \& Option Description Default \& \-\-\-\-\-\- \-\-\-\-\-\-\-\-\-\-\- \-\-\-\-\-\-\- \& \& \-image Specify the image path or URL none \& to use for this feature. \& \& \-image_prefix String to prepend to none \& each image path. You may prepend \& a directory or a partial URL. \& \& \-vertical_spacing Vertical distance from the box 20 \& that shows the physical span of \& of the feature to the top of \& the picture (in pixels). \& \& \-glyph_delegate Glyph to use for the part of \*(Aqgeneric\*(Aq \& the glyph that shows the physical \& span of the feature. .Ve .PP Set \fB\-vertical_spacing\fR to 0 to completely suppress the diagonal lines that connect the physical span of the feature to the image. .SS "Specifying the Image" .IX Subsection "Specifying the Image" The path to the image can be specified in two ways. First, you can place it in the feature itself using a tag named \*(L"image\*(R". Second, you can specify it as a track option using a callback: .PP .Vb 6 \& $panel\->add_track(\e@features, \& \-glyph=>\*(Aqimage\*(Aq, \& \-image => sub { my $feature = shift; \& my $image_path = do_something(); \& return $image } \& ); .Ve .PP You can of course give \-image a constant string, in which case each feature will show the same image. .PP The image can be a file on the local operating system or a \&\s-1URL.\s0 However, \s-1URL\s0 fetching will only work if the \s-1LWP\s0 module is installed on your system. Otherwise the glyph will fail with an error message. .PP If the image is a relative path (it does not begin with a slash or a \&\s-1URL\s0 protocol), then the contents of \-image_prefix will be prepended to it. This allows you to specify images that are relative to a particular directory or a partial \s-1URL.\s0 Example: .PP .Vb 4 \& $panel\->add_track(\e@features, \& \-glyph => \*(Aqimage\*(Aq, \& \-image_prefix => \*(Aqhttp://www.flybase.org/anatomy/image\-browser_files\*(Aq, \& ); .Ve .PP This specifies that each feature's \*(L"image\*(R" tag is to be appended to the partial FlyBase \s-1URL,\s0 thereby saving space. .SS "Glyph Delegation" .IX Subsection "Glyph Delegation" The image glyph consists of two parts: an upper part that shows the extent of the feature in base pair coordinates, and a lower part that shows the image. No scaling of the image is done; its height and width are fixed. .PP By default the upper part uses the \*(L"generic\*(R" glyph, which is a simple rectangle filled with the bgcolor and outlined with the fgcolor. To use a different glyph in the upper part, specify the \-glyph_delegate option, giving the name of the glyph you wish to use. For instance, to use the \*(L"span\*(R" glyph: .PP .Vb 4 \& $panel\->add_track(\e@features, \& \-glyph => \*(Aqimage\*(Aq, \& \-glyph_delegate => \*(Aqspan\*(Aq \& ); .Ve .PP This feature does not work with all glyphs, and in particular requires a recent \s-1CVS\s0 checkout of Bio::Perl to work properly with the \*(L"arrow\*(R", \&\*(L"span\*(R" and \*(L"primers\*(R" glyphs (support for the feature did not make it into version 1.5). .SH "BUGS AND LIMITATIONS" .IX Header "BUGS AND LIMITATIONS" This glyph does not work with \s-1GD::SVG.\s0 If you try to render it onto a \&\s-1GD::SVG\s0 panel, the image will be shown as a gray box. This will be fixed in a future version of \s-1GD::SVG.\s0 .SH "SEE ALSO" .IX Header "SEE ALSO" 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, \&\s-1GD\s0 .SH "AUTHOR" .IX Header "AUTHOR" Lincoln Stein , Todd Harris .PP Copyright (c) 2001 Cold Spring Harbor Laboratory .PP This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See \s-1DISCLAIMER\s0.txt for disclaimers of warranty.