Raw content of Bio::EnsEMBL::Funcgen::Array
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Funcgen::Array
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::Funcgen::Array - A module to represent a nucleotide microarray.
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::Array;
my $array = Bio::EnsEMBL::Funcgen::Array->new(
-NAME => 'Array-1',
-FORMAT => 'Tiled',
-SIZE => '1',
-VENDOR => 'Nimblegen',
-DESCRIPTION => $desc,
-TYPE => 'OLIGO',
-CLASS => 'VENDOR_FORMAT'
);
my $db_adaptor = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(...);
my $array_adaptor = $db_adaptor->get_ArrayAdaptor();
my $array = $array_adaptor->fetch_by_name($array_name)
=head1 DESCRIPTION
An Array object represents a nucleotide (OLIGO, PCR etc.) microarray. The data
(currently the name, format, size, species, vendor and description) are stored
in the array table.
=head1 AUTHOR
This module was created by Nathan Johnson, but is based on the
OligoArray module written by Ian Sealy.
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
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::Array;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Funcgen::Storable;
use vars qw(@ISA);# %VALID_TYPE);
@ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
# Possible types for OligoArray objects
#This should match the vendor enum values?
#%VALID_TYPE = (
# 'AFFY' => 1,
# 'OLIGO' => 1,
#);
=head2 new
Arg [-NAME] : string - the name of this array
Arg [-VENDOR] : string - the vendor of this array (AFFY, NIMBLEGEN etc)
Arg [-TYPE] : string - type of array e.g. OLIGO, PCR
Arg [-FORMAT] : string - the format of this array (TILED, TARGETTED, GENE etc)
Arg [-DESCRIPTION] : strin - description of the array
#array_chips is array of hashes or design_id and name, dbID will be populated on store, this should be a simple object!
Example : my $array = Bio::EnsEMBL::Funcgen::Array->new(
-NAME => 'Array-1',
-FORMAT => 'Tiled',
-SIZE => '1',
-VENDOR => 'Nimblegen',
-TYPE => 'OLIGO',
-DESCRIPTION => $desc,
-CLASS => 'VENDOR_FORMAT',#e.g. AFFY_UTR, ILLUMINA_WG
);
Description: Creates a new Bio::EnsEMBL::Funcgen::Array object.
Returntype : Bio::EnsEMBL::Funcgen::Array
Exceptions : None ? should throw if mandatort params not set/valid
Caller : General
Status : At risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($name, $format, $size, $vendor, $type, $desc, $aclass)
= rearrange( ['NAME', 'FORMAT', 'SIZE', 'VENDOR', 'TYPE', 'DESCRIPTION', 'CLASS'], @_ );
#mandatory params?
#name, format, vendor
#enum on format?
my @stack = caller();
if($self->dbID() && $stack[0] ne "Bio::EnsEMBL::Funcgen::DBSQL::ArrayAdaptor"){
throw("You must use the ArrayAdaptor($stack[0]) to generate Arrays with a dbID i.e. from the DB, as this module accomodates updating which may cause incorrect data if the object is not generated form the DB");
}
throw("Must provide a vendor parameter") if ! $vendor;
throw("Must provide a name parameter") if ! $name;
#any others?
$self->name($name);
$self->format($format) if defined $format;
if(defined $format && $format eq 'EXPRESSION' && ! defined $class){
throw('You must defined a class if you are importing and array with an EXPRESSION format');
}
$self->class(uc($aclass)) if defined $aclass;
$self->size($size) if defined $size;
$self->vendor($vendor);
$self->description($desc) if defined $desc;
$self->type($type) if defined $type;
return $self;
}
=head2 get_all_Probes
Args : None
Example : my $probes = $array->get_all_Probes();
Description: Returns all probes on an array. Needs a database connection.
Returntype : Listref of Bio::EnsEMBL::Funcgen::Probe objects
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub get_all_Probes {
my $self = shift;
if ( $self->dbID() && $self->adaptor() ) {
my $opa = $self->adaptor()->db()->get_ProbeAdaptor();
my $probes = $opa->fetch_all_by_Array($self);
return $probes;
} else {
warning('Need database connection to retrieve Probes');
return [];
}
}
#Nath new get methods
=head2 get_all_ProbeSets
Args : None
Example : my $probesets = $array->get_all_ProbeSets();
Description: Returns all probesets on an array. Needs a database connection.
Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeSets objects
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub get_all_ProbeSets {
my $self = shift;
if ( $self->dbID() && $self->adaptor() ) {
my $opsa = $self->adaptor()->db()->get_ProbeSetAdaptor();
my $probesets = $opsa->fetch_all_by_Array($self);
return $probesets;
} else {
warning('Need database connection to retrieve ProbeSets');
return [];
}
}
#All the array_chip methods will be migrated to ArrayChip.pm
=head2 get_array_chip_ids
Example : my @ac_ids = @{$array->get_array_chip_ids()};
Description: Returns all array_chip_ids for this array.
Returntype : Listref of array_chip ids
Exceptions : Throws if none retrieved
Caller : General
Status : At Risk
=cut
sub get_array_chip_ids {
my $self = shift;
my @ac_ids;
$self->get_ArrayChips();
#now need t
#should we get_ArrayChips is we have none cached?
#this may cause problem
foreach my $achip(values %{$self->{'array_chips'}}){
push @ac_ids, $achip->dbID();
}
if(! @ac_ids){
throw("No array_chip_ids available"); # should this be warn?
}
return \@ac_ids;
}
=head2 get_design_ids
Example : my @design_ids = @{$array->get_design_ids()};
Description: Returns a the design_ids for each array_chip contained within this array
Returntype : list
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub get_design_ids{
my $self = shift;
return [keys %{$self->{'array_chips'}}];
}
=head2 name
Arg [1] : (optional) string - the name of this array
Example : my $name = $array->name();
Description: Getter, setter of the name attribute for Array
objects.
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub name{
my $self = shift;
$self->{'name'} = shift if @_;
#do we need this?
#if ( !exists $self->{'name'} && $self->dbID() && $self->adaptor() ) {
# $self->adaptor->fetch_attributes($self);
#}
return $self->{'name'};
}
=head2 type
Arg [1] : (optional) string - the type of this array
Example : $array->type('OLIGO');
Description: Getter, setter of the type attribute for Array
objects.
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub type{
my $self = shift;
$self->{'type'} = shift if @_;
return $self->{'type'};
}
=head2 format
Arg [1] : (optional) string - the format of the array
Example : my $format = $array->format();
Description: Getter, setter of format attribute for
Array objects e.g. Tiled, Targetted etc...
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub format {
my $self = shift;
$self->{'format'} = shift if @_;
#do we need this?
#if ( !exists $self->{'format'} && $self->dbID() && $self->adaptor() ) {
# $self->adaptor->fetch_attributes($self);
#}
return $self->{'format'};
}
=head2 class
Arg [1] : (optional) string - the class of the array
Example : my $class = $array->class('AFFY_UTR');
Description: Getter, setter of class attribute for
Array objects e.g. AFFY_UTR, AFFY_ST
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub class {
my $self = shift;
$self->{'class'} = shift if @_;
return $self->{'class'};
}
=head2 size
Arg [1] : (optional) int - the number of ? in the array
Example : my $size = $array->size();
Description: Getter of size attribute for Array objects. This
simply counts the constituent ArrayChips
Returntype : int
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub size {
my $self = shift;
return scalar(keys %{$self->{'array_chips'}});
}
=head2 vendor
Arg [1] : (optional) string - the name of the array vendor
Example : my $vendor = $array->vendor();
Description: Getter, setter of vendor attribute for
Array objects.
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub vendor {
my $self = shift;
$self->{'vendor'} = shift if @_;
#do we need this?
#if ( !exists $self->{'vendor'} && $self->dbID() && $self->adaptor() ) {
# $self->adaptor->fetch_attributes($self);
#}
return $self->{'vendor'};
}
=head2 description
Arg [1] : (optional) string - the description of the array
Example : my $size = $array->description();
Description: Getter, setter of description attribute for
Array objects.
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub description {
my $self = shift;
$self->{'description'} = shift if @_;
#do we need this?
#if ( !exists $self->{'description'} && $self->dbID() && $self->adaptor() ) {
# $self->adaptor->fetch_attributes($self);
#}
return $self->{'description'};
}
=head2 get_ArrayChips
Example : my @achips = @{$array->get_ArrayChips()};
Description: Getter, setter and lazy loader of array_chip hashes
Returntype : Arrays of ArrayChip objects
Exceptions : Throws exception if none found for array_id
Caller : General
Status : High Risk - migrate to ArrayChip.pm
=cut
sub get_ArrayChips {
my $self = shift;
#lazy loaded as we won't want this for light DB
#should do meta check and want here
if ( ! exists $self->{'array_chips'}){
if( $self->dbID() && $self->adaptor() ) {
#$self->adaptor->fetch_attributes($self);
#need to do this differently as we're accessing a different table
$self->{'array_chips'} = {};
foreach my $achip(@{$self->adaptor->db->get_ArrayChipAdaptor->fetch_all_by_array_id($self->dbID())}){
$self->{'array_chips'}{$achip->design_id} = $achip;
#%{$self->{'array_chips'}} = %{$self->adaptor->db->get_ArrayAdaptor->_fetch_array_chips_by_array_dbID($self->dbID())};
}
}
else{
throw("Need array dbID and DB connection to retrieve array_chips");
}
}
return [ values %{$self->{'array_chips'}} ];
}
=head2 get_ArrayChip_by_design_id
Arg [1] : (mandatory) int - design_id
Example : my %ac = %{$array->get_ArrayChip_by_design_id('1234')};
Description: Getter for array_chip hashes
Returntype : Hashref
Exceptions : Throws exception if no design_id defined, warns if not part of array
Caller : General
Status : At risk
=cut
sub get_ArrayChip_by_design_id{
my ($self, $design_id) = @_;
#warn "This needs to get the array chip if not defined?? but we're using it to test whether is has been stored same problem as probe_design?";
my ($achip);
throw("Must supply a valid array chip design_id") if (! defined $design_id);
if(defined $self->{'array_chips'}{$design_id}){
$achip = $self->{'array_chips'}{$design_id};
}else{
#No we use this to check whether it has been stored with the array
#warn("should this throw? Array does not contain ArrayChip:$design_id\n");
}
return $achip;
}
=head2 add_ArrayChip
Arg [1] : mandatory - Bio::EnsEMBL::Funcgen::ArrayChip
Example : $array->add_ArrayChip($array_chip);
Description: Setter for array chips
Returntype : None
Exceptions : Throws if arg not a Bio::EnsEMBL::Funcgen::ArrayChip, or Array not stored
Caller : General
Status : Ar risk
=cut
#This uses previosuly stored array_chips withotu warning
#Need to implement fetch_store method?
sub add_ArrayChip{
my ($self, $array_chip) = @_;
throw("You must supply a stored Bio::EnsEMBL::Funcgen::ArrayChip") if(! ($array_chip &&
$array_chip->isa("Bio::EnsEMBL::Funcgen::ArrayChip") &&
$array_chip->dbID()));
if ($self->dbID() && $self->adaptor()){
$self->get_ArrayChips() if (! $self->{'array_chips'});
if(exists $self->{'array_chips'}{$array_chip->design_id}){
$array_chip = $self->{'array_chips'}{$array_chip->design_id};
#warn("Array chip for ".$array_chip->design_id()." already exists, using previous stored array chip\n");
}else{
$self->{'array_chips'}{$array_chip->design_id} = $array_chip;
}
}else{
throw("Array must be stored before adding an array_chip");
}
return;
}
1;
]]>