SYNOPSIS

# create Bio::Coordinate::Pairs or other Bio::Coordinate::MapperIs somehow
$pair1; $pair2;
# add them into a Collection
$collection = Bio::Coordinate::Collection->new;
$collection->add_mapper($pair1);
$collection->add_mapper($pair2);
# create a position and map it
$pos = Bio::Location::Simple->new (-start => 5, -end => 9 );
$res = $collection->map($pos);
$res->match->start == 1;
$res->match->end == 5;
# if mapping is many to one (*>1) or many-to-many (*>*)
# you have to give seq_id not get unrelevant entries
$pos = Bio::Location::Simple->new
(-start => 5, -end => 9 -seq_id=>'clone1');

DESCRIPTION

Generic, context neutral mapper to provide coordinate transforms between two disjoint coordinate systems. It brings into Bioperl the functionality from Ewan Birney's Bio::EnsEMBL::Mapper ported into current bioperl.

This class is aimed for representing mapping between whole chromosomes and contigs, or between contigs and clones, or between sequencing reads and assembly. The submaps are automatically sorted, so they can be added in any order.

To map coordinates to the other direction, you have to swap() the collection. Keeping track of the direction and ID restrictions are left to the calling code.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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

CONTRIBUTORS

Ewan Birney, [email protected]

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

add_mapper

 Title   : add_mapper
 Usage   : $obj->add_mapper($mapper)
 Function: Pushes one Bio::Coordinate::MapperI into the list of mappers.
           Sets _is_sorted() to false.
 Example : 
 Returns : 1 when succeeds, 0 for failure.
 Args    : mapper object

mappers

 Title   : mappers
 Usage   : $obj->mappers();
 Function: Returns or sets a list of mappers.
 Example : 
 Returns : array of mappers
 Args    : array of mappers

each_mapper

 Title   : each_mapper
 Usage   : $obj->each_mapper();
 Function: Returns a list of mappers.
 Example : 
 Returns : list of mappers
 Args    : none

mapper_count

 Title   : mapper_count
 Usage   : my $count = $collection->mapper_count;
 Function: Get the count of the number of mappers stored 
           in this collection
 Example :
 Returns : integer
 Args    : none

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 of all pairs are of the same length.
           Ran automatically.
 Example :
 Returns : boolean
 Args    :

map

 Title   : map
 Usage   : $newpos = $obj->map($pos);
 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 coordinate system
 Args    : integer

_map

 Title   : _map
 Usage   : $newpos = $obj->_map($simpleloc);
 Function: Internal method that does the actual mapping. Called multiple times
           by map() if the location  to be mapped is a split location
 Example :
 Returns : new location in the output coordinate system or undef
 Args    : Bio::Location::Simple

sort

 Title   : sort
 Usage   : $obj->sort;
 Function: Sort function so that all mappings are sorted by
           input coordinate start
 Example :
 Returns : 1
 Args    :

_is_sorted

 Title   : _is_sorted
 Usage   : $newpos = $obj->_is_sorted;
 Function: toggle for whether the (internal) coodinate mapper data are sorted
 Example :
 Returns : boolean
 Args    : boolean