---
name: "Bio::Graphics::Glyph::alignment"
section: "3pm"
platform: "linux"
package: "libbio-graphics-perl"
version: "2.40-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Graphics::Glyph::alignment"
---

# Bio::Graphics::Glyph::alignment(3pm)

The "alignment" glyph

## NAME

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

## SYNOPSIS

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

## DESCRIPTION

This is identical to the "graded\_segments" glyph, and is used for drawing features that consist of discontinuous segments.  The color intensity of each segment is proportionate to the score.

### 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 alignment glyph recognizes the following glyph-specific options:

```
  Option      Description                  Default
  ------      -----------                  -------
  -max_score  Maximum value of the         Calculated
              feature's "score" attribute
  -min_score  Minimum value of the         Calculated
              feature's "score" attribute
```

If max\_score and min\_score are not specified, then the glyph will calculate the local maximum and minimum scores at run time.

## 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

Allen Day \<day@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.