Bio::Graphics::Glyph::merged_alignment(3pm)		User Contributed Perl Documentation	       Bio::Graphics::Glyph::merged_alignment(3pm)

NAME

       Bio::Graphics::Glyph::merged_alignment - The "merged_alignment" glyph

SYNOPSIS

	 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

       This glyph acts like graded_segments but the bgcolor of segments (sub-feature) is controlled by binned scores.  It also supports semantic
       zooming to optimize glyph drawing for larger sequence displays.

   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)

       In addition, the merged-alignment glyph recognizes the following glyph-specific options:

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

	 -max_score  Maximum value of the	  Calculated
		     feature's "score" attribute

	 -min_score  Minimum value of the	  Calculated
		     feature's "score" attribute

	 -bincolors  Colors assigned to bins	  lightgrey powderblue cornflowerblue blue
		     (in order)

	 -bins	     Bins to which scores are	  Calculated
		     assigned

	 -merge_parts				  0 (false)
		     Whether to simplify the
		     alignment at low magnification

	 -max_gap    Do not merge across gaps	  Calculated
		     that exceed this threshold

       If max_score and min_score are not specified, then the glyph will calculate the local maximum and minimum scores at run time.

       If the bins are not specified, they will be calculated based on the number of colors assigned and the local (or user-specified) minimum and
       maximum scores.	Calculated bins are equal in size.

       User-specified bins are expressed as ranges,

	 bins  = 0-50 50-70 70-90 90-100

       where each range means greater than the lower number and less than or equal to the higher number.

   Simplifying the display of alignment features for large segments
       The "merge_parts" option is used for semantic zooming.  Specifically, if features are small and dense, they will not be displayed very well
       for large segments and the color-coding will be lost.  If merge-parts is set to a true value, adjacent alignment parts will be merged until
       a gap exceeding a calculated or user-specified value is encountered.  Unless specified, the maximum gap allowed for merging adjacent
       features is calculated as (L/10000)*(L/500), where L = the length of the sequence displayed in the browser.  The exponentially increasing
       gap threshold allows more aggressive merging of alignment features as the size of the displayed sequence grows larger.

       The score of the merged feature is calculated as a weighted average.  For example, consider two adjacent HSPs that are each 400 bp in
       length and have scores of 60% and 70%.  If the merge_parts option is set to a true value, the two HSPs would be merged in the display to a
       single 800 bp alignment block with an average score of 65%.

       The merge_parts option is turned off by default.

   SAMPLE CONFIGURATION
       Sample gbrowse configuration stanzas for an alignment feature using this glyph.	The scores are assumed to be expressed as percent identity
       (0-100).

	# base configuration
	[BLASTZ]
	feature      = blastz_alignment
	glyph	     = merged_alignment
	bincolors    = #A0A0A0 powderblue cornflowerblue blue
	bins	     = 60-70 70-80 80-90 90-100
	category     = Sequence Similarity Tracks
	height	     = 6
	bump	     = 1
	label	     = 1
	fgcolor      = black
	key	     = BLASTZ

       Semantic zooming with defined maximum gap between merged features for different zoom levels

	# if the displayed segment is >= 20000 in length,
	# use the merge_parts option to simplify the alignment
	# display
	[BLASTZ:20000]
	feature      = blastz_alignment
	merge_parts  = 1
	max_gap      = 50 # do not merge across gaps > 50 bp

	# if the displayed segment is >= 50000 in length
	[BLASTZ:50000]
	feature      = blastz_alignment
	merge_parts  = 1
	max_gap      = 500 # do not merge across gaps > 500 bp

       --OR--

       Semantic zooming with dynamically calculated maximum gap

	# if the displayed segment is >= 20000 in length,
	[BLASTZ:20000]
	feature      = blastz_alignment
	merge_parts  = 1

BUGS

       Please report them.

SEE ALSO

       Bio::Graphics::Panel, Bio::Graphics::Glyph Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD

AUTHOR

       Sheldon McKay <mckays@cshl.edu>

       Copyright (c) 2005 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.

perl v5.14.2							    2012-02-20			       Bio::Graphics::Glyph::merged_alignment(3pm)