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Bio::Coordinate::MapperI(3pm) User Contributed Perl Documentation Bio::Coordinate::MapperI(3pm)


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


version 1.007001


  # not to be used directly


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



 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


 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


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


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


 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


 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)


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.                  - General discussion  - About the mailing lists


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

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:


Heikki Lehvaslaiho <>


This software is copyright (c) by Heikki Lehvaslaiho.

This software is available under the same terms as the perl 5 programming language system itself.

2020-11-24 perl v5.32.0