Provided by: libbio-graphics-perl_2.40-2_all bug

NAME

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

SYNOPSIS

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

DESCRIPTION

       This glyph is used for drawing features that consist of discontinuous segments.  Unlike
       "graded_segments" or "alignment", the segments are a uniform color and not dependent on
       the score of the segment.

   METHODS
       This module overrides the maxdepth() method to return 1 unless explicitly specified by the
       -maxdepth option. This means that modules inheriting from segments will only be presented
       with one level of subfeatures. Override the maxdepth() method to get more levels.

   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)

         -strand_arrow Whether to indicate            0 (false)
                        strandedness

         -hilite       Highlight color                undef (no color)

       In addition, the following glyph-specific options are recognized:

         -draw_dna     If true, draw the dna residues        0 (false)
                        when magnification level
                        allows.

         -draw_target  If true, draw the dna residues        0 (false)
                        of the TARGET sequence when
                        magnification level allows.
                        See "Displaying Alignments".

         -draw_protein_target  If true, draw the protein residues        0 (false)
                        of the TARGET sequence when
                        magnification level allows.
                        See "Displaying Alignments".

         -ragged_extra When combined with -draw_target,      0 (false)
                       draw extra bases beyond the end
                       of the alignment. The value is
                       the maximum number of extra
                       bases.
                       See "Displaying Alignments".

         -ragged_start  Deprecated option.  Use
                        -ragged_extra instead

         -show_mismatch When combined with -draw_target,     0 (false)
                        highlights mismatched bases in
                        the mismatch color.
                        Can be 0 (don't display);
                        1 (display when the DNA fits);
                        or another positive integer
                        (display when the region in
                        view is <= this value).
                        See "Displaying Alignments".

         -mismatch_only When combined with -draw_target,     0 (false)
                        draws only the mismatched bases
                        in the alignment. Implies
                        -show_mismatch.
                        See "Displaying Alignments".

         -mismatch_color The mismatch color to use           'lightgrey'

         -insertion_color The color to use for insertions    'green'
                          relative to the reference.

         -deletion_color The color to use for deletions      'red'
                         relative to the reference.

         -indel_color   The color to use for indels, used   'lightgrey'
                        only if -insertion_color or
                        -deletion_color are absent

         -true_target   Show the target DNA in its native    0 (false)
                        (plus strand) orientation, even if
                        the alignment is to the minus strand.
                        See "Displaying Alignments".

         -realign       Attempt to realign sequences at      0 (false)
                        high mag to account for indels.
                        See "Displaying Alignments".

       If the -draw_dna flag is set to a true value, then when the magnification is high enough,
       the underlying DNA sequence will be shown.  This option is mutually exclusive with
       -draw_target. See Bio::Graphics::Glyph::generic for more details.

       The -draw_target, -ragged_extra, and -show_mismatch options only work with seqfeatures
       that implement the hit() method (Bio::SeqFeature::SimilarityPair). -draw_target will cause
       the DNA of the hit sequence to be displayed when the magnification is high enough to allow
       individual bases to be drawn. The -ragged_extra option will cause the alignment to be
       extended at the extreme ends by the indicated number of bases, and is useful for looking
       for polyAs and cloning sites at the ends of ESTs and cDNAs. -show_mismatch will cause
       mismatched bases to be highlighted in with the color indicated by -mismatch_color. A
       -show_mismatch value of "1" will highlight mismatches only when the base pairs are
       displayed. A positive integer will cause mismatches to be shown whenever the region in
       view is less than or equal to the requested value.

       At high magnifications, minus strand matches will automatically be shown as their reverse
       complement (so that the match has the same sequence as the plus strand of the source dna).
       If you prefer to see the actual sequence of the target as it appears on the minus strand,
       then set -true_target to true.

       Note that -true_target has the opposite meaning from -canonical_strand, which is used in
       conjunction with -draw_dna to draw minus strand features as if they appear on the plus
       strand.

   Displaying Alignments
       When the -draw_target option is true, this glyph can be used to display nucleotide
       alignments such as BLAST, FASTA or BLAT similarities.  At high magnification, this glyph
       will attempt to show how the sequence of the source (query) DNA matches the sequence of
       the target (the hit).  For this to work, the feature must implement the hit() method, and
       both the source and the target DNA must be available.  If you pass the glyph a series of
       Bio::SeqFeature::SimilarityPair objects, then these criteria will be satisified.

       Without additional help, this glyph cannot display gapped alignments correctly.  To
       display gapped alignments, you can use the Bio::Graphics::Brower::Realign module, which is
       part of the Generic Genome Browser package (http://www.gmod.org).  If you wish to install
       the Realign module and not the rest of the package, here is the recipe:

         cd Generic-Genome-Browser-1.XX
         perl Makefile.PL DO_XS=1
         make
         make install_site

       If possible, build the gbrowse package with the DO_XS=1 option.  This compiles a C-based
       DP algorithm that both gbrowse and gbrowse_details will use if they can.  If DO_XS is not
       set, then the scripts will use a Perl-based version of the algorithm that is 10-100 times
       slower.

       The display of alignments can be tweaked using the -ragged_extra, -show_mismatch,
       -true_target, and -realign options.  See the options section for further details.

       There is also a -draw_protein_target option, which is designed for protein to nucleotide
       alignments. It draws the target sequence every third base pair and is supposed to align
       correctly with the forward and reverse translation glyphs. This option is experimental at
       the moment, and may not work correctly, to use with care.

BUGS

       Please report them.

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, GD

AUTHOR

       Lincoln Stein <lstein@cshl.org>

       Copyright (c) 2001 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.