Bio::EnsEMBL::ExternalData::DAS CoordSystem
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Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw )
Synopsis
No synopsis!
Description
No description!
Methods
equalsDescriptionCode
labelDescriptionCode
matches_speciesDescriptionCode
nameDescriptionCode
newDescriptionCode
new_from_hashrefDescriptionCode
new_from_stringDescriptionCode
speciesDescriptionCode
to_string
No description
Code
versionDescriptionCode
Methods description
equalscode    nextTop
  Arg [1]    : Bio::EnsEMBL::ExternalData::DAS::CoordSystem
               The coord system to compare to for equality.
  Example    : if($coord_sys->equals($other_coord_sys)) { ... }
  Description: Compares 2 coordinate systems and returns true if they are
               equivalent.  The definition of equivalent is sharing the same
               name and version, and being species compatible (see the
               matches_species method.
  Returntype : 0 or 1
  Exceptions : none
  Caller     : general
  Status     : Stable
labelcodeprevnextTop
  Arg [1]    : none
  Example    : print $coord->label();
  Description: Getter for the display label of this coordinate system.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
matches_speciescodeprevnextTop
  Arg [1]    : Species string
  Example    : if ( $coord_sys->matches_species( 'Homo_sapiens' ) ) { ... }
  Description: Determines whether the CoordSystem supports a given species. Will
               return if the coordinate system is not species-specific, or is
               specific to the given species.
  Returntype : 1 or 0
  Exceptions : none
  Caller     : general
  Status     : Stable
namecodeprevnextTop
  Arg [1]    : (optional) string $name
  Example    : print $coord_system->name();
  Description: Getter for the name of this coordinate system
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
newcodeprevnextTop
  Arg [..]   : List of named arguments:
               -NAME      - The name of the coordinate system
               -VERSION   - (optional) The version of the coordinate system.
                            Note that if the version passed in is undefined,
                            it will be set to the empty string in the
                            resulting CoordSystem object.
               -SPECIES   - (optional) For species-specific systems
               -LABEL     - (optional) A human-readable label
  Example    : $cs = Bio::EnsEMBL::ExternalData::DAS::CoordSystem->new(
                 -NAME    => 'chromosome',
                 -VERSION => 'NCBI33',
                 -SPECIES => 'Homo_sapiens',
               );
  Description: Creates a new CoordSystem object representing a coordinate
               system.
  Returntype : Bio::EnsEMBL::ExternalData::DAS::CoordSystem
  Exceptions : none
  Caller     : general
  Status     : Stable
new_from_hashrefcodeprevnextTop
  Arg [1]    : Hash reference containing:
               name     - The name of the coordinate system
               version  - (optional) The version of the coordinate system.
                            Note that if the version passed in is undefined,
                            it will be set to the empty string in the
                            resulting CoordSystem object.
               species  - (optional) For species-specific systems
               label    - (optional) A human-readable label
  Example    : $cs = Bio::EnsEMBL::ExternalData::DAS::CoordSystem->new( {
                 name    => 'chromosome',
                 version => 'NCBI33',
                 species => 'Homo_sapiens',
               } );
  Description: Creates a new CoordSystem object representing a coordinate
               system.
  Returntype : Bio::EnsEMBL::ExternalData::DAS::CoordSystem
  Exceptions : none
  Caller     : general
  Status     : Stable
new_from_stringcodeprevnextTop
  Arg [1]    : String containing the following fields, joined by a ":"
               name     - The name of the coordinate system
               version  - (optional) The version of the coordinate system.
                            Note that if the version passed in is undefined,
                            it will be set to the empty string in the
                            resulting CoordSystem object.
               species  - (optional) For species-specific systems
               label    - (optional) A human-readable label
  Example    : $cs = Bio::EnsEMBL::ExternalData::DAS::CoordSystem->new(
                 'chromosome:NCBI33:Homo_sapiens'
               );
               $cs = Bio::EnsEMBL::ExternalData::DAS::CoordSystem->new(
                 'ensembl_gene'
               );
  Description: Creates a new CoordSystem object representing a coordinate
               system.
  Returntype : Bio::EnsEMBL::ExternalData::DAS::CoordSystem
  Exceptions : none
  Caller     : general
  Status     : Stable
speciescodeprevnextTop
  Arg [1]    : none
  Example    : print $coord->species();
  Description: Getter for the species of this coordinate system.  This
               will return an empty string if no species is defined for this
               coordinate system (i.e. it is not species-specific).
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
versioncodeprevnextTop
  Arg [1]    : none
  Example    : print $coord->version();
  Description: Getter for the version of this coordinate system.  This
               will return an empty string if no version is defined for this
               coordinate system.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Methods code
equalsdescriptionprevnextTop
sub equals {
  my $self = shift;
  my $cs = shift;

  unless ( $cs && ref($cs) &&
          ( $cs->isa('Bio::EnsEMBL::ExternalData::DAS::CoordSystem') ||
            $cs->isa('Bio::EnsEMBL::CoordSystem') ) ) {
    throw('Argument must be a CoordSystem');
  }
  
  return ( $self->{'version'} eq $cs->version() &&
           $self->{'name'}    eq $cs->name()    &&
           $self->matches_species( $cs->species ) ) ? 1 : 0;
}
labeldescriptionprevnextTop
sub label {
  my $self = shift;
  return $self->{'label'};
}
matches_speciesdescriptionprevnextTop
sub matches_species {
  my ($self, $species) = @_;
  if ( !$species || !$self->species || $self->species eq $species ) {
    return 1;
  }
  return 0;
}

1;
}
namedescriptionprevnextTop
sub name {
  my $self = shift;
  return $self->{'name'};
}
newdescriptionprevnextTop
sub new {
  my $caller = shift;
  my $class = ref($caller) || $caller;
  my ($name, $version, $species, $label) = rearrange(['NAME','VERSION','SPECIES','LABEL'], @_);

  $name    || throw('The NAME argument is required');
  $version ||= '';
  $species ||= '';
  
  if (!$label) {
    $label = join ' ', map { ucfirst $_ } grep { $_ } (split /_/, $name), $version;
  }
  
  my $self = {
              'name'    => $name,
              'version' => $version,
              'species' => $species,
              'label'   => $label,
             };
  bless $self, $class;

  return $self;
}
new_from_hashrefdescriptionprevnextTop
sub new_from_hashref {
  my $caller = shift;
  my $hash   = shift;
  my $class  = ref($caller) || $caller;
  
  return $class->new( -name    => $hash->{'name'},
                      -version => $hash->{'version'},
                      -species => $hash->{'species'},
                      -label   => $hash->{'label'});
}
new_from_stringdescriptionprevnextTop
sub new_from_string {
  my $caller = shift;
  my $string = shift;
  my $class  = ref($caller) || $caller;

  my ($name, $version, $species, $label) = split /:/, $string, 4;
  return $class->new( -name    => $name,
                      -version => $version,
                      -species => $species,
                      -label   => $label);
}
speciesdescriptionprevnextTop
sub species {
  my $self = shift;
  return $self->{'species'};
}
to_stringdescriptionprevnextTop
sub to_string {
  my $self = shift;
  return join ':', $self->name, $self->version, $self->species, $self->label;
}
versiondescriptionprevnextTop
sub version {
  my $self = shift;
  return $self->{'version'};
}
General documentation
No general documentation available.