Raw content of BioMart::Configuration::VirtualSchema
<![CDATA[# $Id:
#
# BioMart module for BioMart::Configuration::VirtualSchema
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
BioMart::Configuration::VirtualSchema
=head1 SYNOPSIS
Represents the virtualSchema defined in the martRegistry XML
=head1 DESCRIPTION
All BioMart::Configuration::Location implementing objects are contained
within a BioMart::Configuration::VirtualSchema objects in the
BioMart::Registry. At the very least if no virtualSchema is defined in the
registry configuration a single "default" virtualSchema is generated to
contain all Locations and Dataset. Datasets contained in different
virtualSchemas cannot be used in the same BioMart::Query.
=head1 AUTHOR - Damian Smedley
=head1 CONTACT
This module is part of the BioMart project http://www.biomart.org
Questions can be posted to the mart-dev mailing list:
mart-dev@ebi.ac.uk
=head1 METHODS
=cut
package BioMart::Configuration::VirtualSchema;
use strict;
use warnings;
use base qw(BioMart::Root);
use constant NAME => "name";
use constant DISPLAYNAME => "displayName";
use constant TITLES => [ NAME,
DISPLAYNAME,
];
sub _new {
my ($self, @param) = @_;
$self->SUPER::_new(@param);
$self->addParams(TITLES, @param);
$self->attr('default', 0);
$self->attr('locations', []);
$self->attr('visible',1);
}
=head2 name
Usage : my $name = $virtualSchema->name();
$virtualSchemaName->name($newname);
Description: sets/gets the name of the VirtualSchema
Returntype : string name
Exceptions : none
Caller : caller
=cut
sub name {
my ($self, $newName) = @_;
if ($newName) {
$self->setParam(NAME, $newName);
}
return $self->getParam(NAME);
}
=head2 displayName
Usage : my $displayName = $virtualSchema->displayName();
$virtualSchemaDisplayName->displayName($newdisplayName);
Description: sets/gets the displayName of the VirtualSchema
Returntype : string displayName
Exceptions : none
Caller : caller
=cut
sub displayName {
my ($self, $newDisplayName) = @_;
if ($newDisplayName) {
$self->setParam(DISPLAYNAME, $newDisplayName);
}
return $self->getParam(DISPLAYNAME);
}
=head2 default
Usage : my $default = $virtualSchema->default();
$virtualSchemaDefault->default($newname);
Description: sets/gets the default flag of the VirtualSchema
Returntype : string name
Exceptions : none
Caller : caller
=cut
sub default {
my ($self, $newName) = @_;
if ($newName) {
$self->set('default', $newName);
}
return $self->get('default');
}
=head2 visible
Usage : my $visible = $virtualSchema->visible();
$virtualSchema->visible($newname);
Description: sets/gets the visible flag of the VirtualSchema
Returntype : string name
Exceptions : none
Caller : caller
=cut
sub visible {
my ($self, $newName) = @_;
if (defined($newName)) {
$self->set('visible', $newName);
}
return $self->get('visible');
}
=head2 addLocation
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub addLocation {
my ($self, $location) = @_;
my $locations = $self->get('locations');
push @{$locations}, $location;
}
=head2 removeLocation
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub removeLocation {
my ($self,$location) = @_;
my $locations = $self->getAllLocations;
my $i = 0;
foreach my $loc (@$locations){
if ($loc->name eq $location->name){
splice @$locations,$i,1;
last;
}
$i++;
}
}
=head2 getAllLocations
Usage : usage
Description: [deprecated] to be replaced with getAllMarts
Returntype :
Exceptions : none
Caller : caller
=cut
sub getAllLocations {
my $self = shift;
return $self->get('locations');
}
=head2 getAllMarts
Usage : getAllMarts(martusers-required, visible as 1-optional)
Description: Replaced the old getAllLocations call
Returntype :
Exceptions : none
Caller : caller
=cut
sub getAllMarts {
my ($self, $visible) = @_;
if(!$visible)
{
return $self->get('locations');
}
if ($visible == 1)
{
my $allMarts = $self->get('locations');
my $Marts;
foreach my $mart(@$allMarts)
{
if($visible eq $mart->visible())
{
push @{$Marts}, $mart;
}
}
return $Marts;
}
}
sub getMartByName {
my ($self, $name) = @_;
my $allMarts = $self->get('locations');
my $Marts;
foreach my $mart(@$allMarts)
{
if($name eq $mart->name())
{
return $mart;
}
}
return undef;
}
=head2 getDatasetByName
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub getDatasetByName {
my ($self,$datasetName) = @_;
my $retDataset;
LOC:foreach my $location(@{$self->getAllLocations}){
foreach my $dataset(@{$location->getAllDatasets}){
if ($dataset->name eq $datasetName){
$retDataset = $dataset;
last LOC;
}
}
}
return $retDataset;
}
1;
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