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.IX Title "Bio::Graphics::Glyph::alignment 3pm"
.TH Bio::Graphics::Glyph::alignment 3pm "2018-09-21" "perl v5.26.2" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::Graphics::Glyph::alignment \- The "alignment" 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"graded_segments\*(R" glyph, and is used for
drawing features that consist of discontinuous segments.  The
color intensity of each segment is proportionate to the score.
.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
\&
\&  \-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)
.Ve
.PP
In addition, the alignment glyph recognizes the following
glyph-specific options:
.PP
.Vb 2
\&  Option      Description                  Default
\&  \-\-\-\-\-\-      \-\-\-\-\-\-\-\-\-\-\-                  \-\-\-\-\-\-\-
\&
\&  \-max_score  Maximum value of the         Calculated
\&              feature\*(Aqs "score" attribute
\&
\&  \-min_score  Minimum value of the         Calculated
\&              feature\*(Aqs "score" attribute
.Ve
.PP
If max_score and min_score are not specified, then the glyph will
calculate the local maximum and minimum scores at run time.
.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::DB::GFF,
Bio::SeqI,
Bio::SeqFeatureI,
Bio::Das,
\&\s-1GD\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Allen Day <day@cshl.org>.
.PP
Copyright (c) 2001 Cold Spring Harbor Laboratory
.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.