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Manual Reference Pages  -  BIO::MAP::RELATIVEI (3)

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NAME

Bio::Map::RelativeI - Interface for describing what a Position’s coordiantes are
relative to.

CONTENTS

SYNOPSIS



    # do not use this module directly
    # See Bio::Map::Relative for an example of
    # implementation.



DESCRIPTION

A Relative object is used to describe what the co-ordinates (numerical(), start(), end()) of a Position are relative to. By default they are implicitly assumed to be relative to the start of the map the Position is on. But setting the relative() of a Position to one of these objects lets us define otherwise.

FEEDBACK

    Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.



  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists



    Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

    Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:



  https://github.com/bioperl/bioperl-live/issues



AUTHOR - Sendu Bala

Email bix@sendu.me.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

    absolute_conversion



 Title   : absolute_conversion
 Usage   : my $absolute_coord = $relative->absolute_conversion($pos);
 Function: Convert the start co-ordinate of the supplied position into a number
           relative to the start of its map.
 Returns : scalar number
 Args    : Bio::Map::PositionI object



    type



 Title   : type
 Usage   : my $type = $relative->type();
 Function: Get the type of thing we are relative to. The types correspond
           to a method name, so the value of what we are relative to can
           subsequently be found by $value = $relative->$type;

           Note that type is set by the last method that was set, or during
           new().

 Returns : the string map, element or position, or undef
 Args    : none



    map



 Title   : map
 Usage   : my $int = $relative->map();
           $relative->map($int);
 Function: Get/set the distance from the start of the map that the Positions
           co-ordiantes are relative to.
 Returns : int
 Args    : none to get, OR
           int to set; a value of 0 means relative to the start of the map.



    element



 Title   : element
 Usage   : my $element = $relative->element();
           $relative->element($element);
 Function: Get/set the map element (Mappable) the Position is relative to. If
           the Mappable has more than one Position on the Positions map, we
           will be relative to the Mappables first Position on the map.
 Returns : Bio::Map::MappableI
 Args    : none got get, OR
           Bio::Map::MappableI to set



    position



 Title   : position
 Usage   : my $position = $relative->position();
           $relative->position($position);
 Function: Get/set the Position your Position is relative to. Your Position
           will be made relative to the start of this supplied Position. It
           makes no difference what maps the Positions are on.
 Returns : Bio::Map::PositionI
 Args    : none got get, OR
           Bio::Map::PositionI to set



    description



 Title   : description
 Usage   : my $description = $relative->description();
           $relative->description($description);
 Function: Get/set a textual description of what this relative describes.
 Returns : string
 Args    : none to get, OR
           string to set



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perl v5.20.3 BIO::MAP::RELATIVEI (3) 2016-04-05

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