SYNOPSIS¶
# create Bio::Coordinate::Pairs, or any MapperIs, somehow
$pair1; $pair2;
# add them into a Chain
$collection = Bio::Coordinate::Chain->new;
$collection->add_mapper($pair1);
$collection->add_mapper($pair2);
# create a position and map it
$pos = Bio::Location::Simple->new (-start => 5, -end => 9 );
$match = $collection->map($pos);
if ($match) {
sprintf "Matches at %d-%d\n", $match->start, $match->end,
} else {
print "No match\n";
}
DESCRIPTION¶
This class assumes that you have built several mappers and want to link them
together so that output from the previous mapper is the next mappers input.
This way you can build arbitrarily complex mappers from simpler components.
Note that Chain does not do any sanity checking on its mappers. You are solely
responsible that input and output coordinate systems, direction of mapping and
parameters internal to mappers make sense when chained together.
To put it bluntly, the present class is just a glorified foreach loop over an
array of mappers calling the map method.
It would be neat to an internal function that would generate a new single step
mapper from those included in the chain. It should speed things up
considerably. Any volunteers?
map¶
Title : map
Usage : $newpos = $obj->map($pos);
Function: Map the location through all the mappers in the chain.
Example :
Returns : new Location in the output coordiante system
Args : a Bio::Location::Simple object
Inherited methods¶
add_mapper¶
Title : add_mapper
Usage : $obj->add_mapper($mapper)
Function: Pushes one Bio::Coodinate::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 : array of mappers
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 :
sort¶
You do not really want to sort your chain, do you! This function does nothing
other than a warning.