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.\" ========================================================================
.\"
.IX Title "Bio::Graphics::Glyph::generic 3pm"
.TH Bio::Graphics::Glyph::generic 3pm "2019-11-25" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Graphics::Glyph::generic \- The "generic" glyph
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is identical to the \*(L"box\*(R" glyph except that it will draw the
subparts of features that contain subfeatures.  The subparts are not
connected \*(-- use the \*(L"segments\*(R" glyph for that.  \*(L"Generic\*(R" is the
default glyph used when not otherwise specified.
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
This module overrides the \fBmaxdepth()\fR method to return 0 unless the
\&\-maxdepth option is provided explicitly. This means that any module
that inherits from generic will need to override \fBmaxdepth()\fR again in
order to draw subfeatures. In general, those implementing
multi-segmented feature glyphs should inherit from
Bio::Graphics::Glyph::segments, which allows for one level of descent.
.PP
In addition, the following new methods are implemented:
.IP "\fBlabelfont()\fR, \fBdescfont()\fR, \fBlabelwidth()\fR, \fBdescriptionwidth()\fR" 4
.IX Item "labelfont(), descfont(), labelwidth(), descriptionwidth()"
Return the font, width for the label or description.
.IP "\fBlabel()\fR" 4
.IX Item "label()"
Return the glyph label text (printed above the glyph).
.IP "\fBdescription()\fR" 4
.IX Item "description()"
Return the glyph description text (printed below the glyph).
.IP "\fBdraw_translation()\fR" 4
.IX Item "draw_translation()"
Draw the protein translation of the feature (assumes that the feature is attached to a \s-1DNA\s0 sequence).
.IP "\fBdraw_sequence()\fR" 4
.IX Item "draw_sequence()"
Draw the sequence of the feature (either \s-1DNA\s0 or protein).
.SS "\s-1OPTIONS\s0"
.IX Subsection "OPTIONS"
The following options are standard among all Glyphs.  See
Bio::Graphics::Glyph for a full explanation.
.PP
.Vb 2
\&  Option      Description                      Default
\&  \-\-\-\-\-\-      \-\-\-\-\-\-\-\-\-\-\-                      \-\-\-\-\-\-\-
\&
\&  \-fgcolor      Foreground color               black
\&
\&  \-bgcolor      Background color               turquoise
\&
\&  \-fillcolor    Synonym for \-bgcolor
\&
\&  \-linewidth    Line width                     1
\&
\&  \-height       Height of glyph                10
\&
\&  \-font         Default font                   gdSmallFont
\&
\&  \-label_font   Font used for label            gdSmallFont
\&
\&  \-desc_font    Font used for description      gdSmallFont
\&
\&  \-connector    Connector type                 0 (false)
\&
\&  \-connector_color
\&                Connector color                black
\&
\&  \-pad_top      Top padding                    0
\&
\&  \-pad_bottom   Bottom padding                 0
\&
\&  \-label        Whether to draw a label        0 (false)
\&
\&  \-label_position Where to draw the label      "top" (default) or "left"
\&
\&  \-description  Whether to draw a description  0 (false)
\&
\&  \-strand_arrow Whether to indicate            0 (false)
\&                 strandedness
\&
\&  \-hilite       Highlight color                undef (no color)
\&
\&  \-draw_dna     If true, draw the dna residues        0 (false)
\&                 when magnification level
\&                 allows.
\&
\&  \-canonical_strand If true, draw the dna residues        0 (false)
\&                 as they appear on the plus strand
\&                 even if the feature is on the minus
\&                 strand.
.Ve
.PP
\&\-pad_top and \-pad_bottom allow you to insert some blank space between
the glyph's boundary and its contents.  This is useful if you are
changing the glyph's height dynamically based on its feature's score.
.SH "BUGS"
.IX Header "BUGS"
Please report them.
.SH "SEE ALSO"
.IX Header "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::Graphics::Glyph::xyplot,
Bio::DB::GFF,
Bio::SeqI,
Bio::SeqFeatureI,
Bio::Das,
\&\s-1GD\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Allen Day <day@cshl.org>,
Lincoln Stein <lincoln.stein@gmail.com>
.PP
Copyright (c) 2001 Cold Spring Harbor Laboratory
Copyright (c) 2010 Ontario Institute for Cancer Research
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.