Bio::Graphics::Glyph::segments Bio::Graphics::Glyph::segments is a Perl module that conatins the 'segments' glyph.
Download

Bio::Graphics::Glyph::segments Ranking & Summary

Bio::Graphics::Glyph::segments Tags

Perl module Segments glyph bioperl segments glyph BioPerl graphics

Bio::Graphics::Glyph::segments Description

Bio::Graphics::Glyph::segments is a Perl module that conatins the 'segments' glyph. Bio::Graphics::Glyph::segments is a Perl module that conatins the "segments" glyph.SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >.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.METHODSThis 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.OPTIONSThe 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_color The mismatch color to use '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. Requirements: · Perl

Bio::Graphics::Glyph::segments Related Software