Raw content of Bio::EnsEMBL::Funcgen::Experiment
<![CDATA[
=head1 NAME
Bio::EnsEMBL::Funcgen::Experiment
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::Experiment;
my $array = Bio::EnsEMBL::Funcgen::Experiment->new(
-ADAPTOR => $self,
-NAME => $name,
-GROUP => $group,
-DATE => $date,
-PRIMARY_DESIGN_TYPE => $p_design_type,
-DESCRIPTION => $description,
);
my $db_adaptor = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(...);
my $exp_adaptor = $db_adaptor->get_ExperimentAdaptor();
my $exp = $exp_adaptor->fetch_by_name($exp_name)
=head1 DESCRIPTION
An Experiment object represents an experiment instance . The data
are stored in the experiment, egroup, target, design_type and
experimental_variable tables.
=head1 AUTHOR
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
################################################################################
package Bio::EnsEMBL::Funcgen::Experiment;
use warnings;
use strict;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Funcgen::Storable;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
=head2 new
Arg [-NAME]: string - the name of this experiment
Arg [-GROUP]: string - the name of the experimental group
Arg [-GROUP_ID]: int - the dbID of the experimental group
Arg [-DATE]: string - the date of the experiment (format?)
Arg [-PRIMARY_DESIGN_TYPE]: string - MGED term for the primary design of teh experiment e.g. binding_site_identification
Arg [-DESCRIPTION]: string - of the experiment
Example : my $array = Bio::EnsEMBL::Funcgen::Experiment->new(
-NAME => $name,
-GROUP => $group,
-DATE => $date,
-PRIMARY_DESIGN_TYPE => $p_design_type,
-DESCRIPTION => $description,
);
Description: Creates a new Bio::EnsEMBL::Funcgen::Experiment object.
Returntype : Bio::EnsEMBL::Funcgen::Experiment
Exceptions : None ? Should throw if mandatory params not set
Caller : General
Status : Medium Risk
=cut
#experimental_variables?
#design_type
#target(s)?
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($name, $group_id, $group, $date, $p_dtype, $desc, $xml_id, $xml)
= rearrange( ['NAME', 'GROUP_ID', 'GROUP', 'DATE', 'PRIMARY_DESIGN_TYPE', 'DESCRIPTION', 'MAGE_XML', 'MAGE_XML_ID'], @_ );
$self->name($name) if defined $name;
$self->group_id($group_id) if defined $group_id;
$self->group($group) if defined $group;
$self->date($date) if defined $date;
$self->primary_design_type($p_dtype) if defined $p_dtype;
$self->description($desc) if defined $desc;
$self->mage_xml_id($xml_id) if defined $xml_id;
$self->mage_xml($xml) if defined $xml;
#Need to add mandatory params check here!!
#name, group or group_id
return $self;
}
### GENERIC ACCESSOR METHODS ###
=head2 name
Arg [1]: string - the name of this experiment
Example: $exp->name('Experiment-1');
Description: Getter/Setter for the experiment name
Returntype : string
Exceptions : None
Caller : General
Status : Stable
=cut
sub name{
my ($self) = shift;
$self->{'name'} = shift if(@_);
return $self->{'name'};
}
=head2 group_id
Arg [1]: int - the group dbID corresponding to this experiment
Example: $exp->group_db_id('1');
Description: Getter/Setter for the group_db_id
Returntype : int
Exceptions : None
Caller : General
Status : Stable
=cut
sub group_id{
my ($self) = shift;
$self->{'group_id'} = shift if(@_);
return $self->{'group_id'};
}
=head2 mage_xml
Arg [1]: string(optional) - MAGE XML
Example: my $xml = $exp->mage_xml();
Description: Getter/Setter for the mage_xml attribute
Returntype : string
Exceptions : None
Caller : General
Status : at risk
=cut
sub mage_xml{
my ($self) = shift;
$self->{'mage_xml'} = shift if(@_);
#use fetch_attrs?
if(! exists $self->{'mage_xml'} && $self->mage_xml_id()){
$self->{'mage_xml'} = $self->adaptor->fetch_mage_xml_by_Experiment($self);
}
return (exists $self->{'mage_xml'}) ? $self->{'mage_xml'} : undef;
}
=head2 mage_xml_id
Arg [1]: int (optional) - mage_xml_id
Example: $exp->group_db_id('1');
Description: Getter/Setter for the mage_xml attribute
Returntype : string
Exceptions : None
Caller : General
Status : at risk
=cut
sub mage_xml_id{
my $self = shift;
$self->{'mage_xml_id'} = shift if @_;
return $self->{'mage_xml_id'};
}
=head2 group
Arg [1]: optional - Bio::EnsEMBL::Funcgen::Group
Example: my $exp_group_name = $exp->group->name();
Description: Getter/Setter for the group
Returntype : Bio::EnsEMBL::Funcgen::Group
Exceptions : None
Caller : General
Status : At risk
=cut
sub group{
my ($self) = shift;
if(@_){
$self->{'group'} = shift;
}elsif(! exists $self->{'group'}){
#this should be group_adaptor->fetch_by_dbID($self->group_id());
throw("Not yet implemented group adaptor");
}
return $self->{'group'};
}
=head2 date
Arg [1]: optional - date, format yyyy-mm-dd
Example: $exp->date('2006-06-09');
Description: Getter/Setter for the date
Returntype : date string
Exceptions : None ? should throw/warn if format not correct
Caller : General
Status : Medium
=cut
sub date{
my $self = shift;
if(@_){
#Need to validate format here
$self->{'date'} = shift;
}
return $self->{'date'};
}
=head2 description
Arg [1]: string - the experiment description
Example: $exp->description("Human chromosome X TFBS identification");
Description: Getter/Setter for the experiment description
Returntype : string
Exceptions : None
Caller : General
Status : Stable
=cut
sub description{
my $self = shift;
$self->{'description'} = shift if(@_);
return $self->{'description'};
}
=head2 primary_design_type
Arg [1]: string - MGED term for primary design type
Example: $exp->primary_design_type('binding_site_identification');
Description: Getter/Setter for the primary design type
Returntype : string
Exceptions : None ? should throw if not MGED term
Caller : General
Status : At risk
=cut
sub primary_design_type{
my ($self) = shift;
if(@_){
#warn "Need to validate design_types against MGED";
$self->{'primary_design_type'} = shift;
}
return $self->{'primary_design_type'};
}
#These convenience methods are to provide a registry for the experimental chips of the experiment
=head2 get_ExperimentalChips
Example: my $exp_chips = @{$exp->get_ExperimentalChips()}
Description: Retrieves all ExperiemntalChips
Returntype : Listref of ExperimentalChips
Exceptions : None
Caller : General
Status : At risk
=cut
sub get_ExperimentalChips{
my ($self) = shift;
#should this also store echips?
#Need to retrieve all from DB if not defined, then check whether already present and add and store if not
#what about immediate access to dbID
#should we separate and have add_ExperimentalChip?
if(! exists $self->{'experimental_chips'}){
$self->{'experimental_chips'} = {};
#need to warn about DBAdaptor here?
foreach my $echip(@{$self->adaptor->db->get_ExperimentalChipAdaptor->fetch_all_by_experiment_dbID($self->dbID())}){
$self->{'experimental_chips'}->{$echip->unique_id()} = $echip;
}
}
#is this returning a list or a listref?
return [values %{$self->{'experimental_chips'}}];
}
=head2 add_ExperimentalChip
Example : $exp_chip = $exp->add_ExperimentalChip($exp_chip)
Description : Adds and stores an ExperiemntalChip for this Experiment
Returntype : Bio::EnsEMBL::Funcgen::ExperimentalChip
Exceptions : Throws is not passed a valid stored Bio::EnsENBML::Funcgen::ExperimentalChip
Caller : General
Status : At risk
=cut
sub add_ExperimentalChip{
my ($self, $echip) = @_;
throw("Must pass a valid stored Bio::EnsEMBL::Funcgen::ExperimentalChip object")
if(! $echip->isa("Bio::EnsEMBL::Funcgen::ExperimentalChip") || ! $echip->dbID());
if(! exists $self->{'experimental_chips'}){
$self->get_ExperimentalChips();
$self->{'experimental_chips'}->{$echip->unique_id()} = $echip;
#do this here without checking to avoid probelm of retrieving first stored chip
}elsif(exists $self->{'experimental_chips'}->{$echip->unique_id()}){
warn("You cannot add the same ExperimentalChip(".$echip->unique_id().")to an Experiment more than once, check your code");
}else{
$self->{'experimental_chips'}->{$echip->unique_id()} = $echip;
}
return;
}
=head2 get_ExperimentalChip_by_unique_id
Example: $exp_chip = $exp->add_ExperimentalChip($exp_chip)
Description: Adds and stores an ExperiemntalChip for this Experiment
Returntype : Bio::EnsEMBL::Funcgen::ExperimentalChip
Exceptions : Throws if no uid supplied
Caller : General
Status : At risk
=cut
sub get_ExperimentalChip_by_unique_id{
my ($self, $uid) = @_;
my ($echip);
throw("Must supply a ExperimentalChip unque_id") if(! defined $uid);
$self->{'experimental_chips'} || $self->get_ExperimentalChips();
if(exists $self->{'experimental_chips'}->{$uid}){
$echip = $self->{'experimental_chips'}->{$uid};
}
#should we warn here if not exists?
return $echip;
}
=head2 get_ExperimentalChip_unique_ids
Example: foreach my $uid(@{$self->experiment->get_ExperimentalChip_unique_ids()}){ ... }
Description: retrieves all ExperimentalChip unique_ids
Returntype : ListRef
Exceptions : None
Caller : General
Status : At risk
=cut
sub get_ExperimentalChip_unique_ids{
my $self = shift;
$self->{'experimental_chips'} || $self->get_ExperimentalChips();
return [keys %{ $self->{'experimental_chips'}}];
}
#should we add a methods to return just the
#methods?
#lazy load design_types and exp_variables
#target? Is this a one to one?
1;
]]>