Raw content of BioMart::Configuration::AttributeList
<![CDATA[# $Id: AttributeList.pm,v 1.4 2008/04/09 12:52:33 syed Exp $
#
# BioMart module for BioMart::Configuration::AttributeList
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
BioMart::Configuration::AttributeList
=head1 SYNOPSIS
Stores an array of attribute objects, in order.
=head1 DESCRIPTION
Stores an array of attribute objects. Used to handle the behaviour of
exportables in the system. When linking two Datasets together, the
BioMart::QueryRunner object will add the BioMart::AttributeList object
exported from the Exporting Dataset to the Query targeted to the
Exporting Dataset.
=head1 AUTHOR - Arek Kasprzyk, Syed Haider, Richard Holland, Darin London, Damian Smedley
=head1 CONTACT
This module is part of the BioMart project http://www.biomart.org
Questions can be posted to the mart-dev mailing list:
mart-dev@ebi.ac.uk
=head1 METHODS
=cut
package BioMart::Configuration::AttributeList;
use strict;
use warnings;
use Digest::MD5;
use base qw(BioMart::Configuration::Attribute);
use constant LINKNAME => "linkName";
use constant LINKVERSION => "linkVersion";
use constant ATTRIBUTESTRING => "attribute_string";
use constant ORDERBYSTRING => "orderby_string";
use constant TYPE => "type";
use constant TITLES => [
LINKNAME,
LINKVERSION,
ATTRIBUTESTRING,
ORDERBYSTRING,
TYPE
];
=head2 _new
Usage : minimal:
my $alist = BioMart::AttributeList->new();
with name and dataSetName
my $alist = BioMart::AttributeList->new(
'name' => $name,
'dataSetName' => $subName
);
To be used as a Link Exportable (note orderby_string is
optional):
my $alist = BioMart::AttributeList->new(
'name' => $name,
'dataSetName' => $subName,
'linkName' => $linkName,
'attribute_string' => $attribute_string,
'orderby_string' => $orderby_string
);
Description: creates a new AttributeList object capable of storing an
array of Attribute objects
Returntype : BioMart::Configuration::AttributeList
Exceptions : none
Caller : caller
=cut
sub _new {
my ($self, @param) = @_;
$self->SUPER::_new(@param);
$self->addParams(TITLES, @param);
$self->attr('attributes', []);
$self->attr('orderby_attributes', []);
$self->attr('default', 0);
}
=head2 linkName
Usage : my $linkName = $alist->linkName;
$alist->linkName($newLinkName);
Description : get/set the linkName of this BioMart::AttributeList object.
Returntype : scalar $linkName
Exceptions : none
Caller : caller
=cut
sub linkName {
my ($self, $name) = @_;
if ($name) {
$self->setParam(LINKNAME, $name);
}
return $self->getParam(LINKNAME);
}
=head2 linkVersion
Usage : my $linkVersion = $alist->linkVersion;
$alist->linkVersion($newLinkVersion);
Description : get/set the linkVersion of this BioMart::AttributeList
object.
Returntype : scalar $linkVersion
Exceptions : none
Caller : caller
=cut
sub linkVersion {
my ($self, $name) = @_;
if ($name) {
$self->setParam(LINKVERSION, $name);
}
return $self->getParam(LINKVERSION);
}
=head2 attributeString
Usage : my $attributeString = $alist->attributeString;
$alist->attributeString($newAttString);
Description : get/set the attributeString of this BioMart::AttributeList
object.
Returntype : scalar $attributeString
Exceptions : none
Caller : caller
=cut
sub attributeString {
my ($self, $name) = @_;
if ($name) {
$self->setParam(ATTRIBUTESTRING, $name);
}
return $self->getParam(ATTRIBUTESTRING);
}
=head2 orderByString
Usage : my $orderByString = $alist->orderByString;
$alist->orderByString($newOrderByString);
Description : get/set the orderByString of this BioMart::AttributeList
object.
Returntype : scalar $orderByString (a comma separated list of
BioMart::Configuration::Attribute names)
Exceptions : none
Caller : caller
=cut
sub orderByString {
my ($self, $name) = @_;
if ($name) {
$self->setParam(ORDERBYSTRING, $name);
}
return $self->getParam(ORDERBYSTRING);
}
=head2 type
Usage : $exp->type();
Description : get/set for the exportable type
object.
Returntype : string
Exceptions : none
Caller : caller
=cut
sub type {
my ($self, $name) = @_;
if ($name) {
$self->setParam(TYPE, $name);
}
return $self->getParam(TYPE);
}
=head2 addAttribute
Usage : $alist->addAttribute($att);
Description: adds a BioMart::Attribute object to the AttributeList,
maintaining the order of addition.
Returntype : none
Exceptions : none
Caller : caller
=cut
sub addAttribute {
my ($self, $attribute) = @_;
my $attributes = $self->get('attributes');
push @{$attributes}, $attribute;
$self->set('attributes', $attributes);
}
=head2 getAllAttributes
Usage : my $atts = $alist->getAllAttributes;
Description : get all Attributes added to this AttributeList.
Primarily used by BioMart::ResultTable to
support getFieldByName and getIndexByName, but
may also be used by DatasetI objects which
override or ignore the default toSQL method.
Returntype : array_ref of BioMart::Attribute objects
Exceptions : none
Caller : BioMart::ResultTable, and BioMart::DatasetI implementatiions.
=cut
sub getAllAttributes {
my $self = shift;
return $self->get('attributes');
}
sub getAttributeByName {
my ($self,$name) = @_;
my $attribute;
my $attributes = $self->get('attributes');
foreach (@$attributes){
if ($_->name eq $name){
$attribute = $_;
last;
}
}
return $attribute;
}
=head2 addOrderByAttribute
Usage : $alist->addSortByAttribute($att);
Description: adds a BioMart::Attribute object to the AttributeList
sortBy list, maintaining the order of addition.
Returntype : none
Exceptions : none
Caller : caller
=cut
sub addOrderByAttribute {
my ($self, $attribute) = @_;
my $attributes = $self->get('orderby_attributes');
push @{$attributes}, $attribute;
$self->set('orderby_attributes', $attributes);
}
=head2 toSQL
Usage : my $sql = $alist->toSQL;
Description: returns a SQL stub for all the attributes stored in the
AttributeList
Returntype : string
Exceptions : none
Caller : caller
=cut
sub toSQL {
# gets each attribute, inserts ',' in between
my $self = shift;
my $sql;
my $attributes = $self->get('attributes');
foreach my $attribute (@$attributes){
$sql .= ' '.$attribute->toSQL().',';
}
chop $sql;
return $sql;
}
=head2 toOrderBySQL
Usage : my $sql = $alist->toOrderBySQL;
Description: returns a SQL stub for all the attributes stored in the
AttributeList sortBy list.
Returntype : string
Exceptions : none
Caller : caller
=cut
sub toOrderBySQL {
# gets each attribute, inserts ',' in between
my $self = shift;
my $sql;
my $attributes = $self->get('orderby_attributes');
foreach my $attribute (@$attributes){
$sql .= ' '.$attribute->toSQL().',';
}
chop $sql;
return $sql;
}
=head2 setDefault
Usage : $alist->setDefault;
Description: sets this AttributeList as the default
Returntype : none
Exceptions : none
Caller : caller
=cut
sub setDefault {
my $self = shift;
$self->set('default',1);
}
=head2 unSetDefault
Usage : $alist->unSetDefault;
Description: this BioMart::AttributeList will no longer be the default.
Returntype : none
Exceptions : none
Caller : caller
=cut
sub unSetDefault {
my $self = shift;
$self->set('default',0);
}
=head2 defaultList
Usage : no arguments
Description: returns 1 if this AttributeList is the default, otherwise 0
Returntype : 0,1
Exceptions : none
Caller : caller
=cut
sub defaultList {
my $self = shift;
return $self->get('default');
}
sub _hashCode {
my $self = shift;
my $digest = Digest::MD5->new;
$digest->add($self->name) if ($self->name);
$digest->add($self->linkName) if ($self->linkName);
$digest->add($self->dataSetName) if ($self->dataSetName);
my $atts = $self->get('attributes');
foreach my $att (@{$atts}) {
$digest->add($att->hashCode);
}
$digest->add($self->defaultList);
return $digest->hexdigest;
}
1;
]]>