Bio::Coordinate Chain
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Coordinate::Chain - Mapping locations through a chain of coordinate mappers
Package variables
No package variables defined.
Included modules
Bio::Coordinate::Collection Bio::Coordinate::MapperI
  # 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"; }
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?
No description
Methods description
mapcode    nextTop
 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
Methods code
sub map {
    my ($self,$value) = @_;

    $self->throw("Need to pass me a value.")
	unless defined $value;
    $self->throw("I need a Bio::Location, not [$value]")
	unless $value->isa('Bio::LocationI');
    $self->throw("No coordinate mappers!")
	unless $self->each_mapper;

    my $res = Bio::Coordinate::Result->new();

    foreach my $mapper ($self->each_mapper) {

	my $res = $mapper->map($value);
	return unless $res->each_match;
	$value = $res->match;

   return $value;
sub sort {
   my ($self) = @_;
   $self->warn("You do not really want to sort your chain, do you!\nDoing nothing.");

General documentation
Mailing ListsTop
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Please direct usage questions or support issues to the mailing list:
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address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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
AUTHOR - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
Ewan Birney,
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Inherited methodsTop
 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
 Title   : mappers
Usage : $obj->mappers();
Function: Returns or sets a list of mappers.
Example :
Returns : array of mappers
Args : array of mappers
 Title   : each_mapper
Usage : $obj->each_mapper();
Function: Returns a list of mappers.
Example :
Returns : array of mappers
Args : none
 Title   : swap
Usage : $obj->swap;
Function: Swap the direction of mapping;input <-> output
Example :
Returns : 1
Args :
 Title   : test
Usage : $obj->test;
Function: test that both components of all pairs are of the same length.
Ran automatically.
Example :
Returns : boolean
Args :