Raw content of Bio::EnsEMBL::Pipeline::Flag
<![CDATA[# Perl module for Bio::EnsEMBL::Pipeline::DBSQL::Flag
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Pipeline::Flag
=head1 SYNOPSIS
my $flag = Bio::EnsEMBL::Pipeline::Flag->new(
'-type' => 'gene',
'-ensembl_id' => 12345,
'-goalAnalysis' => $analysis_object,
);
=head1 DESCRIPTION
Object to allow flagging of sequences for further analysis.
The flag consists of the dbID of the object to be flagged, the name of the
table in which it is stored and the analysis that you would like to
pass the object to.
=head1 CONTACT
Post general queries to ensembl-dev@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Pipeline::Flag;
use vars qw(@ISA);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use strict;
@ISA = qw( Bio::EnsEMBL::Root );
=head2 Constructor
Title : new
Usage : ...Flag->new($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.
=cut
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;
}
=head2 goalAnalysis
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
=cut
sub goalAnalysis {
my ($self,$arg) = @_;
( defined $arg ) &&
( $self->{'_goal'} = $arg );
return $self->{'_goal'};
}
=head2 dbID
Title : dbID
Usage : $self->dbID($dbID);
Function: Get/set method for the dbID of this flag.
Returns : Scalar
Args : Scalar
=cut
sub dbID {
my ( $self, $dbID ) = @_;
( defined $dbID ) &&
( $self->{'_dbID'} = $dbID );
return $self->{'_dbID'};
}
=head2 ensemblID
Title : ensemblID
Usage : $self->ensemblID($ensemblID);
Function: Get/set method for the dbID of the object to be flagged
Returns : Scalar
Args : Scalar
=cut
sub ensembl_id {
my ( $self, $id) = @_;
( defined $id ) &&
( $self->{'_id'} = $id );
return $self->{'_id'};
}
=head2 type
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
=cut
sub type {
my ( $self, $type) = @_;
( defined $type ) &&
( $self->{'_type'} = $type );
$self->{'_type'};
}
=head2 adaptor
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
=cut
sub adaptor {
my ( $self, $adaptor ) = @_;
( defined $adaptor ) &&
( $self->{'_adaptor'} = $adaptor );
return $self->{'_adaptor'};
}
1;
]]>