Bio::EnsEMBL::Pipeline Flag
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvsRaw content
Summary
Bio::EnsEMBL::Pipeline::Flag
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
strict
Inherit
Bio::EnsEMBL::Root
Synopsis
  my $flag = Bio::EnsEMBL::Pipeline::Flag->new(
					       '-type'         => 'gene',
					       '-ensembl_id'   => 12345,
					       '-goalAnalysis' => $analysis_object,
					       );
Description
Object to allow flagging of sequences for further analysis.
The flag consists of the dbID of the object to be flagged, the name of the
table in which it is stored and the analysis that you would like to
pass the object to.
Methods
adaptorDescriptionCode
dbIDDescriptionCode
ensembl_id
No description
Code
goalAnalysisDescriptionCode
new
No description
Code
typeDescriptionCode
Methods description
adaptorcode    nextTop
  Title   : adaptor
  Usage   : $self->adaptor($adaptor);
  Function: Get/set method for the flag adaptor set is private
  Returns : Bio::EnsEMBL::Pipeline::DBSQL::FlagAdaptor
  Args    : Bio::EnsEMBL::Pipeline::DBSQL::FlagAdaptor
dbIDcodeprevnextTop
  Title   : dbID
  Usage   : $self->dbID($dbID);
  Function: Get/set method for the dbID of this flag.
  Returns : Scalar
  Args    : Scalar
goalAnalysiscodeprevnextTop
  Title   : goalAnalysis
  Usage   : $self->goalAnalysis($analysis);
  Function: Get/set method for the goal analysis object of this flag.
  Returns : Bio::EnsEMBL::Analysis
  Args    : Bio::EnsEMBL::Analysis
typecodeprevnextTop
  Title   : type
  Usage   : $self->type('table_name');
  Function: Get/set method for the name of the table that the flagged object sits in
  Returns : Scalar
  Args    : Scalar
Methods code
adaptordescriptionprevnextTop
sub adaptor {
  my ( $self, $adaptor ) = @_;
  ( defined $adaptor ) &&
    ( $self->{'_adaptor'} = $adaptor );
  return $self->{'_adaptor'};
}

1;
}
dbIDdescriptionprevnextTop
sub dbID {
  my ( $self, $dbID ) = @_;
  ( defined $dbID ) &&
    ( $self->{'_dbID'} = $dbID );
  return $self->{'_dbID'};
}
ensembl_iddescriptionprevnextTop
sub ensembl_id {
  my ( $self, $id) = @_;
  ( defined $id ) &&
    ( $self->{'_id'} = $id );
  return $self->{'_id'};
}
goalAnalysisdescriptionprevnextTop
sub goalAnalysis {
  my ($self,$arg) = @_;

  ( defined $arg ) &&
    ( $self->{'_goal'} = $arg );
  return $self->{'_goal'};
}
newdescriptionprevnextTop
sub new {
  my ($class,@args) = @_;
  my $self = $class->SUPER::new(@args);

  $self->{'_goal'} = {}; # Container for analysis object
  $self->{'_dbID'} = 0;  # Container for scalar dbID of the flag
  $self->{'_id'} = 0;    # Container for scalar dbID of object to be flagged
  $self->{'_type'} = ""; # Name of the table the object is stored in ie: gene 
  $self->{'_adaptor'} = {}; # Container for FlagAdaptor object

  my ( $goal,$type, $ensembl_id, $adaptor, $dbID ) =
    Bio::EnsEMBL::Utils::Argument->rearrange( [ qw ( GOALANALYSIS
			      TYPE
			      ENSEMBL_ID
			      ADAPTOR
			      DBID
			     ) ], @args );
  $self->throw( "Wrong parameter" ) unless $goal->isa( "Bio::EnsEMBL::Analysis");
  $self->type( $type );
  $self->goalAnalysis( $goal );
  $self->adaptor( $adaptor );
  $self->dbID( $dbID );
  $self->ensembl_id( $ensembl_id  );
  return $self;
}
typedescriptionprevnextTop
sub type {
  my ( $self, $type) = @_;
  ( defined $type ) &&
    ( $self->{'_type'} = $type );
  $self->{'_type'};
}
General documentation
CONTACTTop
Post general queries to ensembl-dev@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
ConstructorTop
  Title   : new
  Usage   : ...Flag->new($analysis);
  Function: Constructor for Flag object
  Returns : Bio::EnsEMBL::Pipeline::Flag
  Args    : A Bio::EnsEMBL::Analysis object.
            adaptor and dbid only used from the adaptor.
ensemblIDTop
  Title   : ensemblID
  Usage   : $self->ensemblID($ensemblID);
  Function: Get/set method for the dbID of the object to be flagged
  Returns : Scalar
  Args    : Scalar