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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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  # not to be used directly

DESCRIPTION

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

FEEDBACK

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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

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Email: heikki-at-bioperl-dot-org

APPENDIX

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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)
BioPerl documentation Contained in the BioPerl distribution. 
#
# bioperl module for Bio::Coordinate::MapperI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...

package Bio::Coordinate::MapperI;
use strict;

# Object preamble - inherits from Bio::Root::RootI

use base qw(Bio::Root::RootI);




sub in {
   my ($self,$value) = @_;

   $self->throw_not_implemented();

}



sub out {
   my ($self,$value) = @_;

   $self->throw_not_implemented();
}


sub swap {
   my ($self) = @_;

   $self->throw_not_implemented();

}


sub test {
   my ($self) = @_;

   $self->throw_not_implemented();
}



sub map {
   my ($self,$value) = @_;

   $self->throw_not_implemented();

}


sub return_match {
   my ($self,$value) = @_;
   if( defined $value) {
       $value ? ( $self->{'_return_match'} = 1 ) :
                ( $self->{'_return_match'} = 0 );
   }
   return $self->{'_return_match'} || 0 ;
}

1;