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.
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
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