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Bio::Graphics::Glyph::UsereContributed Perl DocuBio::Graphics::Glyph::trace(3)

NAME
       Bio::Graphics::Glyph::trace - A glyph that visualizes a trace file

SYNOPSIS
	use Bio::Graphics;
	use Bio::Seq;
	use Bio::SeqFeature::Generic;

	my $bsg	= 'Bio::SeqFeature::Generic';

	my $seq	   = Bio::Seq->new(-length=>1000);

	my $whole  = $bsg->new(-display_name =>	'Clone82',
			       -start	     =>	1,
			       -end	     =>	$seq->length);

	my $trace1 = $bsg->new(-start	     =>	100,
			       -end	     =>	300,
			       -display_name =>	'Excretory System',
			       -tag=>{
				     trace=>"/path/to/trace/file.scf"
				     }
			      );

	my $trace2 = $bsg->new(-start	     =>	500,
			       -end	     =>	800,
			       -display_name =>	'Expression Pattern',
			       -tag=>{
				     trace=>"http://localhost/traces/file2.scf"
				     }
			      );

	my $panel = Bio::Graphics::Panel->new(-length	 => $seq->length,
					      -width	 => 800,
					      -truecolor => 1,
					      -key_style => 'between',
					      -pad_left	 => 10,
					      -pad_right => 10,
					     );

	$panel->add_track($whole,
			  -glyph    => 'arrow',
			  -double   => 1,
			  -tick	    => 2,
			  -label    => 1,
			  );

	$panel->add_track([$trace1,$trace2],
			  -glyph    => 'trace',
			  -label    => 1,
			  -key	     =>	'Example traces');

	binmode	STDOUT;
	print $panel->png;

DESCRIPTION
       This glyph parses and displays trace information	from a file.  A
       generic glyph is	used to	show where the trace is	located	and when the
       display is zoomed in enough to see the sequence,	the trace will be
       drawn.

       The trace file can only be in SCF format.  The file can be located on
       the local filesystem or located at a remote URL (provided that you have
       the LWP module installed).

       Until an	alignment feature is added to this glyph, the feature start
       and end must correspond exactly with the	begining and end of the	called
       sequence.  Meaning that even if the starting sequence is	poor and
       doesn't match the sequence, it must still be included.

       The figure below	illustrates this.  The trace and the reference
       sequence	align from points "b" to "c".  The positions "A" and "D" need
       to be calculated	and used in order for the trace	to line	up correctly.

		    A	   b	     c	   D
	 ref -------------------------------------------------
			   |||||||||||
	 trace	    ------------------------

       The glyph may be	modified in the	future to avoid	this hassle (and it
       should still be compatible with the method described above).

   OPTIONS
       The following options are standard among	all Glyphs.  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)

	 -hilite       Highlight color		      undef (no	color)

       The following additional	options	are available to the "image" glyph:

	 Option		   Description			     Default
	 ------		   -----------			     -------

	 -trace		   Specify the trace path or URL     none
			   to use for this feature

	 -trace_prefix	   String to prepend to		     none
			   each	trace path. You	may prepend
			   a directory or a partial URL.

	 -trace_height	   The height in pixels	that the     90
			   trace will be drawn

	 -vertical_spacing Vertical distance from the box    20
			   that	shows the physical span	of
			   the feature to the top of the
			   picture (in pixels)

	 -glyph_delegate   Glyph to use	when zoomed out	too  'generic'
			   far for the trace to	be drawn

	 -a_color	   Color of the	line representing    'green'
			   Adenine on the trace

	 -c_color	   Color of the	line representing    'blue'
			   Cytosine on the trace

	 -g_color	   Color of the	line representing    'black'
			   Guanine on the trace

	 -t_color	   Color of the	line representing    'red'
			   Thymine on the trace

	 -show_border	   Show	the black border from	     0
			   around the trace

	 -abi_scale	   The scale factor for	abi	     1
			   formatted files.  This is
			   multiplied against the max
			   trace value to determine the
			   hight of peaks.

   Specifying the Trace
       The path	to the trace file can be specified in two ways.	First, you can
       place it	in the feature itself using a tag named	"trace". Second, you
       can specify it as a track option	using a	callback:

	 $panel->add_track(\@features,
			   -glyph=>'trace',
			   -trace => sub { my $feature = shift;
					   my $trace_path = do_something();
					   return $trace }
			   );

       You can of course give -trace a constant	string,	in which case each
       feature will show the same trace.

       The trace can be	a file on the local operating system or	a URL.
       However,	URL fetching will only work if the LWP module is installed on
       your system.  Otherwise the glyph will fail with	an error message.

       If the trace is a relative path (it does	not begin with a slash or a
       URL protocol), then the contents	of -trace_prefix will be prepended to
       it. This	allows you to specify traces that are relative to a particular
       directory or a partial URL. Example:

	 $panel->add_track(\@features,
			   -glyph => 'trace',
			   -trace_prefix => 'http://localhost/anatomy/trace-browser_files',
			  );

       This specifies that each	feature's "trace" tag is to be appended	to the
       partial localhost URL, thereby saving space.

   Glyph Delegation
       The trace 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 trace.	 The upper part	will always be displayed.  The lower
       part will only display if zoomed	close enough to	see the	sequence.

       By default the upper part uses the "generic" 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 "span" glyph:

	 $panel->add_track(\@features,
			   -glyph	   => 'trace',
			   -glyph_delegate => 'span'
			  );

       This feature does not work with all glyphs, and in particular requires
       a recent	CVS checkout of	Bio::Perl to work properly with	the "arrow",
       "span" and "primers" glyphs (support for	the feature did	not make it
       into version 1.5).

BUGS AND LIMITATIONS
       See the DESCRIPTION for an explaination of how to align the trace with
       the reference.

       The trace looks a little	off when the feature is	on the negative	strand
       of the reference.  This is because the letters are on the oppisite side
       of the position line.  This issue should	be addressed.

       This glyph uses it's own	version	of the Bio::Graphics::Panel method,
       map_pt(), due to	that method not	behaving as needed.  The new copied
       method is called	"trace_map_pt".

       If the trace file is gzipped, it	will unzip it without destroying the
       gzipped file.  However, it will also not	remove the newly created file.
       This will only be an issue when the files are stored locally, since web
       accessed	trace files are	stored as temp files anyway.

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::image, 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
       Ben Faga	<faga@cshl.edu>, Lincoln Stein <lstein@cshl.org>, Todd Harris
       <harris@cshl.org>

       Copyright (c) 2006 Cold Spring Harbor Laboratory

       This package and	its accompanying libraries is free software; you can
       redistribute it and/or modify it	under the terms	of the GPL (either
       version 1, or at	your option, any later version)	or the Artistic
       License 2.0.  Refer to LICENSE for the full license text. In addition,
       please see DISCLAIMER.txt for disclaimers of warranty.

perl v5.32.0			  2020-08-29	Bio::Graphics::Glyph::trace(3)

NAME | SYNOPSIS | DESCRIPTION | BUGS AND LIMITATIONS | SEE ALSO | AUTHOR

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