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 _
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)