/ 
bioperl-1.5.2_004-RCd
/ Bio::Graphics::Glyph::ruler_arrow

NAME

Bio::Graphics::Glyph::ruler_arrow - glyph for drawing an arrow as ruler (5' and 3' are marked as label)

NAME

Bio::Graphics::Glyph::arrow - The "ruler_arrow" glyph

SYNOPSIS

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

DESCRIPTION

This glyph draws arrows. Label, if requested, will be 5' and 3' at both ends and tick scale is printed if no_tick_label option is set and tick option set. Depending on options, the arrows can be labeled, be oriented vertically or horizontally, or can contain major and minor ticks suitable for use as a scale.

OPTIONS

In addition to the common options, the following glyph-specific options are recognized:

  Option      Description               Default
  ------      -----------               -------

  -tick       Whether to draw major         0
              and minor ticks.
	      0 = no ticks
	      1 = major ticks
	      2 = minor ticks
  -label      5' at start, 3' at end        0
              above arrow
  -both       5', 3' above,                 0
              and 3', 5' below arrow
  -direction  0 = ruler is plus strand      0
              -1 = ruler is minus strand

  -parallel   Whether to draw the arrow     true
	      parallel to the sequence
	      or perpendicular to it.

  -northeast  Force a north or east         true
	      arrowhead(depending 
	      on orientation)

  -east       synonym of above

  -southwest  Force a south or west         true
	      arrowhead(depending 
	      on orientation)

  -west       synonym of above

  -double     force-doubleheaded arrow

  -base       Draw a vertical base at the   false
              non-arrowhead side

  -scale      Reset the labels on the arrow false
              to reflect an externally 
              established scale.

Set -parallel to false to display a point-like feature such as a polymorphism, or to indicate an important location. If the feature start == end, then the glyph will draw a single arrow at the designated location:

^
|

Otherwise, there will be two arrows at the start and end:

^              ^
|              |

Scale: Pass in a externally established scale to reset the labels on the arrow. This is particularly useful for manually constructed images where the founding parameters of the panel are not 1-based. For example, a genetic map interval ranging from 0.1 - 0.3 can be constructed by first multiplying every value by 100. Passing

arrow(-scale=>100);

will draw tick marks labelled appropriately to your external scale.

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

Shengqiang Shu <sshu@bdgp.lbl.gov> Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2001 BDGP, 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.