Bio::Coordinate::MapperI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Coordinate::MapperI - Interface describing coordinate mappers

SYNOPSIS

   # not to be used directly
 
 

DESCRIPTION

MapperI defines methods for classes capable for mapping locations between coordinate systems.

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 lists 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 the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

APPENDIX

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

in

  Title   : in
  Usage   : $obj->in('peptide');
  Function: Set and read the input coordinate system.
  Example :
  Returns : value of input system
  Args    : new value (optional), Bio::LocationI
 
 

out

  Title   : out
  Usage   : $obj->out('peptide');
  Function: Set and read the output coordinate system.
  Example :
  Returns : value of output system
  Args    : new value (optional), Bio::LocationI
 
 

swap

  Title   : swap
  Usage   : $obj->swap;
  Function: Swap the direction of mapping: input <-> output)
  Example :
  Returns : 1
  Args    :
 
 

test

  Title   : test
  Usage   : $obj->test;
  Function: test that both components are of same length
  Example :
  Returns : ( 1 | undef )
  Args    :
 
 

map

  Title   : map
  Usage   : $newpos = $obj->map($loc);
  Function: Map the location from the input coordinate system
            to a new value in the output coordinate system.
  Example :
  Returns : new value in the output coordiante system
  Args    : Bio::LocationI
 
 

return_match

  Title   : return_match
  Usage   : $obj->return_match(1);
  Function: A flag to turn on the simplified mode of
            returning only one joined Match object or undef
  Example :
  Returns : boolean
  Args    : boolean (optional)