Bio::Graphics::Glyph::segments man page on Fedora

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Bio::Graphics::Glyph::UsereContributed Perl DBio::Graphics::Glyph::segments(3)

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.
			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'

	 -indel_color	The color to use for small indels.   'lightgrey'

	 -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
       (default lightgray).

       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.

perl v5.14.1			  2011-07-22 Bio::Graphics::Glyph::segments(3)
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