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Summary

Bio::EnsEMBL::Compara::Production::DnaCollection

Package variables

Included modules

Synopsis

Description

DnaColelction is an object to hold a super-set of DnaFragChunk, and/or DnaFragChunkSet
objects. Used in production to encapsulate particular genome/region/chunk/group DNA set
from the others. To allow system to blast against self, and isolate different
chunk/group sets of the same genome from each other.

Methods

Methods description

 Title   : adaptor
 Usage   :
 Function: getter/setter of the adaptor for this object
 Example :
 Returns :
 Args    :

  Example    : $count = $chunkSet->count;
  Description: returns count of DnaFragChunks in this set
  Returntype : int
  Exceptions :
  Caller     :

  Arg [1]    : int $dbID (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :

  Arg [1]    : string $description (optional)
  Example    :
  Description:
  Returntype : string
  Exceptions :
  Caller     :

  Arg [1]    : string $dump_loc (optional)
  Example    :
  Description:
  Returntype : string
  Exceptions :
  Caller     :

  Example    : @dna = @{$dnaCOllection->get_all_dna_objects};
  Description: returns array reference to all the DnaFragChunkand DnaFragChunkSet objects in this set
  Returntype : reference to array of Bio::EnsEMBL::Compara::Production::DnaFragChunk(DnaFragChunkSet) objects
  Exceptions :
  Caller     :

  Example    : @dnafrag_ids = @{$dnaCOllection->get_all_dnafrag_ids};
  Description: returns array reference to all the dnafrag_ids in this set
  Returntype : reference to array of integers
  Exceptions :
  Caller     :

Methods code

sub adaptor {

  my $self = shift;
  $self->{'_adaptor'} = shift if(@_);
  return $self->{'_adaptor'};

}

sub add_dna_object {

  my ($self, $object) = @_;
  
  return unless(defined($object));
  unless($object->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunk') or
         $object->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunkSet'))
  {
    $self->throw(
      "arg must be a [Bio::EnsEMBL::Compara::Production::DnaFragChunk] ".
      "or [Bio::EnsEMBL::Compara::Production::DnaFragChunk] not a [$object]");
  }
  if ($object->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunk')) {
    unless ($self->{'_dnafrag_id_hash'}->{$object->dnafrag_id}) {
      push @{$self->{'_dnafrag_id_list'}}, $object->dnafrag_id;
      $self->{'_dnafrag_id_hash'}->{$object->dnafrag_id} = 1;
    }
  }
  if ($object->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunkSet')) {
    foreach my $dc (@{$object->get_all_DnaFragChunks}) {
      unless ($self->{'_dnafrag_id_hash'}->{$dc->dnafrag_id}) {
        push @{$self->{'_dnafrag_id_list'}}, $dc->dnafrag_id;
        $self->{'_dnafrag_id_hash'}->{$dc->dnafrag_id} = 1;
      }
    }
  }

  push @{$self->{'_object_list'}}, $object;

}

sub count {

  my $self = shift;
  return scalar(@{$self->{'_object_list'}});

}

sub dbID {

  my $self = shift;
  $self->{'_dbID'} = shift if(@_);
  return $self->{'_dbID'};

}

sub description {

  my $self = shift;
  $self->{'_description'} = shift if(@_);
  return $self->{'_description'};

}

sub dump_loc {

  my $self = shift;
  $self->{'_dump_loc'} = shift if(@_);
  return $self->{'_dump_loc'};

}

sub get_all_dna_objects {

  my $self = shift;
  return $self->{'_object_list'};

}

sub get_all_dnafrag_ids {

  my $self = shift;
  return $self->{'_dnafrag_id_list'};
}

1;

}

sub new {

  my ($class, @args) = @_;

  my $self = {};
  bless $self,$class;

  $self->{'_object_list'} = [];
  $self->{'_dnafrag_id_list'} = [];
  $self->{'_dnafrag_id_hash'} = {};

  if (scalar @args) {
    #do this explicitly.
    my ($dbid, $description, $adaptor) = rearrange([qw(DBID DESCRIPTION ADAPTOR)], @args);

    $self->dbID($dbid)               if($dbid);
    $self->description($description) if($description);
    $self->adaptor($adaptor)         if($adaptor);
  }

  return $self;

}

General documentation

Jessica Severin <jessica@ebi.ac.uk>

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _