NAME

Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets.

VERSION

version 1.007001

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.

ATTRIBUTES

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

METHODS

new

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

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

sort

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

INTERNAL METHODS

_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

_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

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 list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/%%7Bdist%7D

AUTHOR

Heikki Lehvaslaiho <heikki@bioperl.org>

COPYRIGHT

This software is copyright (c) by Heikki Lehvaslaiho.

This software is available under the same terms as the perl 5 programming language system itself.

cpanm Bio::Coordinate

perl -MCPAN -e shell
install Bio::Coordinate