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Summary

Bio::EnsEMBL::ExternalData::DAS::FeatureGroup

Package variables

Synopsis

  my $g = Bio::EnsEMBL::ExternalData::DAS::FeatureGroup->new( {
    'group_id'    => 'group1',
    'group_label' => 'Group 1',
    'group_type'  => 'transcript',
    'note'        => [ 'Something interesting' ],
    'link'        => [
                      { 'href' => 'http://...',
                        'txt'  => 'Group Link'  }
                     ],
    'target'      => [
                      { 'target_id'    => 'Seq 1',
                        'target_start' => '400',
                        'target_stop'  => '800'  }
                     ]
  } );
  
  printf "Group ID:     %s\n", $g->display_id();
  printf "Group Label:  %s\n", $g->display_label();
  printf "Group Type:   %s\n", $g->type_label();
  
  for my $l ( @{ $g->links() } ) {
    printf "Group Link:   %s -> %s\n", $l->{'href'}, $l->{'txt'};
  }
  
  for my $n ( @{ $g->notes() } ) {
    printf "Group Note:   %s\n", $n;
  }
  
  for my $t ( @{ $g->targets() } ) {
    printf "Group Target: %s:%s,%s\n", $t->{'target_id'},
                                       $t->{'target_start'},
                                       $t->{'target_stop'};
  }

Description

An object representation of a DAS feature group.
The constructor is designed to work with the output of the DAS features command,
as obtained from the Bio::Das::Lite module.
See http://www.biodas.org/documents/spec.html for more information about DAS
and its data types.

Methods

Methods description

  Arg [1]    : none
  Example    : print $g->display_id();
  Description: This method returns the DAS group identifier.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : print $g->display_label();
  Description: This method returns the DAS group label.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : @links = @{ $g->links() };
  Description: This method returns the DAS group external links.
  Returntype : arrayref of { href=>$, txt=>$ } hashes
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : Hash reference (see SYNOPSIS for details and example)
  Description: Constructs a new Bio::EnsEMBL::ExternalData::DAS::FeatureGroup.
  Returntype : Bio::EnsEMBL::ExternalData::DAS::FeatureGroup
  Exceptions : none
  Caller     : Bio::EnsEMBL::ExternalData::DAS::Feature
  Status     : Stable

  Arg [1]    : none
  Example    : @notes = @{ $g->notes() };
  Description: This method returns the DAS group notes.
  Returntype : arrayref of strings
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : @targets = @{ $g->targets() };
  Description: This method returns the DAS group targets.
  Returntype : arrayref of { target_id=>$, target_start=>$, target_stop=>$ } hashes
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

  Arg [1]    : none
  Example    : print $g->type_label();
  Description: This method returns the DAS group type label.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

Methods code

sub display_id {

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

}

sub display_label {

  my $self = shift;
  return $self->{'group_label'} || $self->display_id;

}

sub links {

  my $self = shift;
  return $self->{'link'} || [];

}

sub new {

  my $proto = shift;
  my $class = ref $proto || $proto;
  my $raw   = shift;
  
  my $self = {};
  for my $key qw( group_id group_label
                  group_type
                  note link target ) {
    $self->{$key} = $raw->{$key} if exists $raw->{$key};
  }
  
  bless $self, $class;
  return $self;

}

sub notes {

  my $self = shift;
  return $self->{'note'} || [];

}

sub targets {

  my $self = shift;
  return $self->{'target'} || [];
}

1;

}

sub type_label {

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

# The following are zero-to-many, thus return arrayrefs:

}

General documentation

Andy Jenkinson

Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk