Provided by: libbio-graphics-perl_2.40-6_all bug

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.