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:

https://redmine.open-bio.org/projects/bioperl/

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)

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq