/ 
bioperl-1.2
/ Bio::Coordinate::Pair

NAME

Bio::Coordinate::Pair - Continuous match between two coordinate sets

SYNOPSIS

use Bio::Location::Simple;
use Bio::Coordinate::Pair;

my $match1 = Bio::Location::Simple->new 
    (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
my $match2 = Bio::Location::Simple->new
    (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
my $pair = Bio::Coordinate::Pair->new(-in => $match1,
					-out => $match2,
				        -negative => 0, # false, default
# location to match
$pos = Bio::Location::Simple->new 
    (-start => 25, -end => 25, -strand=> -1 );

# results are in Bio::Coordinate::Result
# they can be Matches and Gaps; are  Bio::LocationIs
$res = $pair->map($pos);
$res->isa('Bio::Coordinate::Result');
$res->each_match, 1;
$res->each_gap, 0;
$res->each_location, 1;
$res->match->start, 5;
$res->match->end, 5;
$res->match->strand, -1;
$res->match->seq_id, 'peptide';

DESCRIPTION

Class

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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR - Heikki Lehvaslaiho

Email: heikki@ebi.ac.uk Address:

EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom

CONTRIBUTORS

Additional contributors names and emails here

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    :

strand

Title   : strand
Usage   : $obj->strand;
Function: Get strand value for the pair
Example :
Returns : ( 1 | 0 | -1 )
Args    :

test

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

map

Title   : map
Usage   : $newpos = $obj->map(5);
Function: Map the location from the input coordinate system 
          to a new value in the output coordinate system.
Example :
Returns : new Bio::LocationI in the output coordiante system
Args    : Bio::LocationI object