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lib/Bio/EnsEMBL/ChainedAssemblyMapper.pm  view on Meta::CPAN

The ChainedAssemblyMapper is an extension of the regular AssemblyMapper
that allows for mappings between coordinate systems that require
multi-step mapping.  For example if explicit mappings are defined
between the following coordinate systems,

  chromosome <-> contig
  contig     <-> clone

the ChainedAssemblyMapper would be able to perform implicit mapping
between the chromosome and clone coordinate systems.  This should be
transparent to the user of this module, and users should not even
realise that they are using a chained assembly mapper as opposed to a
normal assembly mapper.

=head1 METHODS

=cut

package Bio::EnsEMBL::ChainedAssemblyMapper;
$Bio::EnsEMBL::ChainedAssemblyMapper::VERSION = '113.0.0';
use strict;

lib/Bio/EnsEMBL/IdMapping/Cache.pm  view on Meta::CPAN

sub get_by_key {
  my $self = shift;
  my $name = shift;
  my $type = shift;
  my $key = shift;

  throw("You must provide a cache name (e.g. genes_by_id.") unless $name;
  throw("You must provide a cache type.") unless $type;
  throw("You must provide a cache key (e.g. a gene dbID).") unless $key;

  # transparently load cache from file unless already loaded
  unless ($self->{'instance'}->{'loaded'}->{"$type"}) {
    $self->read_and_merge($type);
  }

  return $self->{'cache'}->{$type}->{$name}->{$key};
}

sub get_by_name {
  my $self = shift;
  my $name = shift;
  my $type = shift;

  throw("You must provide a cache name (e.g. genes_by_id.") unless $name;
  throw("You must provide a cache type.") unless $type;
  
  # transparently load cache from file unless already loaded
  unless ($self->{'instance'}->{'loaded'}->{$type}) {
    $self->read_and_merge($type);
  }

  return $self->{'cache'}->{$type}->{$name} || {};
}


sub get_count_by_name {
  my $self = shift;
  my $name = shift;
  my $type = shift;

  throw("You must provide a cache name (e.g. genes_by_id.") unless $name;
  throw("You must provide a cache type.") unless $type;
  
  # transparently load cache from file unless already loaded
  unless ($self->{'instance'}->{'loaded'}->{$type}) {
    $self->read_and_merge($type);
  }

  return scalar(keys %{ $self->get_by_name($name, $type) });
}


sub find_common_coord_systems {
  my $self = shift;