Bio::Coordinate::Collection(3pm) User Contributed Perl Documentation Bio::Coordinate::Collection(3pm)
NAME
Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets
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.
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
CONTRIBUTORS
Ewan Birney, birney@ebi.ac.uk
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
perl v5.14.2 2012-03-02 Bio::Coordinate::Collection(3pm)