Raw content of BioMart::Configuration::BaseFilter
<![CDATA[# $Id: BaseFilter.pm,v 1.5.2.1 2008/07/04 16:12:59 syed Exp $
#
# BioMart module for BioMart::Configuration::BaseFilter
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
BioMart::Configuration::BaseFilter
=head1 SYNOPSIS
Base Interface for all BioMart filters.
=head1 DESCRIPTION
Base Interface for BioMart filters
=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::BaseFilter;
use strict;
use warnings;
use Digest::MD5;
use base qw(BioMart::Root);
use constant NAME => "name";
use constant DISPLAYNAME => "displayName";
use constant DESCRIPTION => "description";
use constant DATASETNAME => "dataSetName";
use constant IMAGEURL => "imageURL";
use constant INTERFACE => "interface";
use constant BUTTONURL => "buttonURL";
use constant SETATTRIBUTEPAGE => "setAttributePage";
use constant DEFAULTON => "defaultOn";
use constant SETATTRIBUTE => "setAttribute";
use constant DISPLAYTYPE => "displayType";
use constant MULTIPLEVALUES => "multipleValues";
use constant STYLE => "style";
use constant GRAPH => "graph";
use constant AUTOCOMPLETION => "autoCompletion";
use constant TYPE => "type";
use constant FILTERCOLLECTION => "filterCollection";
use constant POINTEDFROMDATASET => "pointedFromDataset";
use constant POINTEDFROMINTERFACE => "pointedFromInterface";
use constant DEPENDSON => "dependsOn";
use constant DEPENDSONTYPE => "dependsOnType";
use constant HIDEDISPLAY => "hideDisplay";
use constant LEGAL_QUALIFIERS => "legalQualifiers";
use constant TITLES => [
NAME,
DISPLAYNAME,
DESCRIPTION,
DATASETNAME,
IMAGEURL,
INTERFACE,
BUTTONURL,
SETATTRIBUTEPAGE,
DEFAULTON,
TYPE,
SETATTRIBUTE,
DISPLAYTYPE,
MULTIPLEVALUES,
STYLE,
GRAPH,
AUTOCOMPLETION,
POINTEDFROMDATASET,
POINTEDFROMINTERFACE,
DEPENDSON,
DEPENDSONTYPE,
HIDEDISPLAY,
LEGAL_QUALIFIERS
];
=head2 _new
Usage : minimal (users should next set the name and dataSetName with the
appropriate setter methods):
my $filt =
BioMart::Configuration::BaseFilter_implementation->new();
with name, and dataSetName
my $filt =
BioMart::Configuration::BaseFilter_implementation->new(
'name' => $name,
'dataSetName' => $subName);
Description: create a new BaseFilter object
Returntype : BioMart::Configuration::BaseFilter
Exceptions : none
Caller : general
=cut
sub _new {
my ($self, @param) = @_;
$self->SUPER::_new(@param);
$self->addParams(TITLES, @param);
$self->attr('options', []);
$self->attr('dependency',[]);
}
sub _init {
my ($self, @param) = @_;
$self->SUPER::_init(@param);
my $proto = shift @param;
$self->attr('options', $proto->getAllOptions);
}
=head2 addOption
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub addOption {
my ($self, $option) = @_;
my $options = $self->get('options');
push @{$options}, $option;
}
=head2 addOptions
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub addOptions {
my ($self, $new_options) = @_;
my $options = $self->get('options');
push @{$options}, @{$new_options};
}
=head2 getAllOptions
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub getAllOptions {
my $self = shift;
return $self->get('options');
}
=head2 name
Usage : my $name = $filt->name; $filt->name($newName);
Description: get/set for the name of the filter
Returntype : scalar $name
Exceptions : none
Caller : caller
=cut
sub name {
my ($self, $value) = @_;
if ($value){
$self->setParam(NAME, $value);
}
return $self->getParam(NAME);
}
=head2 displayName
Usage : Arg [1] - (optional) string $display_name
Description: get/set for display name
Returntype : string
Exceptions : none
Caller : general
=cut
sub displayName {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(DISPLAYNAME, $value);
}
return $self->getParam(DISPLAYNAME);
}
=head2 description
Usage : Arg [1] - (optional) string $description
Description: get/set for description
Returntype : string
Exceptions : none
Caller : general
=cut
sub description {
# stores description
my ($self, $value) = @_;
if ($value){
$self->setParam(DESCRIPTION, $value);
}
return $self->getParam(DESCRIPTION);
}
=head2 table
Usage :
Description: returns the table name associated with this filter;
Returntype : String table name
Exceptions : none
Caller : caller
=cut
sub table {
#my $self = shift;
#my $attribute = $self->get('attribute');
#return $attribute->table;
return "";
}
=head2 dependsOn
Usage : Arg [1] - (optional) string $dependsOn delimited by commas
Description: get/set for dependsOn atribute(s) for a dataset
Returntype : string
Exceptions : none
Caller : general
=cut
sub dependsOn {
my ($self, $value) = @_;
if ($value){
$self->setParam(DEPENDSON, $value);
}
return $self->getParam(DEPENDSON);
}
=head2 dependsOnType
Usage : Arg [1] - (optional) string $dependsOnType
Description: get/set for dependsOnType - all or any are acceptable.
Returntype : string
Exceptions : none
Caller : general
=cut
sub dependsOnType {
my ($self, $value) = @_;
if ($value){
$self->setParam(DEPENDSONTYPE, $value);
}
return $self->getParam(DEPENDSONTYPE);
}
=head2 addDependency
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub addDependency {
my ($self, $resolvedDependency) = @_;
push @{$self->get('dependency')}, $resolvedDependency;
}
=head2 dependencies
Usage : usage
Description: Description
Returntype :
Exceptions : none
Caller : caller
=cut
sub dependencies {
my $self = shift;
return $self->get('dependency');
}
=head2 imageURL
Usage : Arg [1] - (optional) string $imageURL
Description: get/set for imageURL, a relative URL.
This is only used by MartView.
Returntype : string
Exceptions : none
Caller : general
=cut
sub imageURL {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(IMAGEURL, $value);
}
return $self->getParam(IMAGEURL);
}
=head2 buttonURL
Usage : Arg [1] - (optional) string $buttonURL
Description: get/set for display name
Returntype : string
Exceptions : none
Caller : general
=cut
sub buttonURL {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(BUTTONURL, $value);
}
return $self->getParam(BUTTONURL);
}
=head2 pointedFromDataset
Usage : Arg [1] - (optional) string $pointedFromDataset
Description: get/set for pointedFromDataset atribute(s) for a dataset
Returntype : string
Exceptions : none
Caller : general
=cut
sub pointedFromDataset {
my ($self, $value) = @_;
if ($value){
$self->setParam(POINTEDFROMDATASET, $value);
}
return $self->getParam(POINTEDFROMDATASET);
}
=head2 pointedFromInterface
Usage : Arg [1] - (optional) string $pointedFromInterface
Description: get/set for pointedFromInterface atribute(s) for a dataset
Returntype : string
Exceptions : none
Caller : general
=cut
sub pointedFromInterface {
my ($self, $value) = @_;
if ($value){
$self->setParam(POINTEDFROMINTERFACE, $value);
}
return $self->getParam(POINTEDFROMINTERFACE);
}
=head2 setAttributePage
Usage : Arg [1] - (optional) string $setAttributePage
Description: get/set for display name
Returntype : string
Exceptions : none
Caller : general
=cut
sub setAttributePage {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(SETATTRIBUTEPAGE, $value);
}
return $self->getParam(SETATTRIBUTEPAGE);
}
=head2 dataSetName
Usage : my $subName = $filt->dataSetName;
$filt->dataSetName($newName);
Description : get/set the name of the dataSet providing this Filter
to the user.
Returntype : scalar $name
Exceptions : none
Caller : caller
=cut
sub dataSetName {
my ($self, $name) = @_;
if ($name) {
$self->setParam(DATASETNAME, $name);
}
return $self->getParam(DATASETNAME);
}
=head2 interface
Usage : my $interface = $att->interface; $att->interface->($newName);
Description: get/set for the name of the interface which hosts this
filter.
Returntype : scalar $name
Exceptions : none
Caller : general
=cut
sub interface {
my ($self, $value) = @_;
if ($value){
$self->setParam(INTERFACE, $value);
}
return $self->getParam(INTERFACE);
}
=head2 defaultOn
Usage : Arg [1] - (optional) string $defaultOn
Description: get/set for default on
Returntype : string
Exceptions : none
Caller : general
=cut
sub defaultOn {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(DEFAULTON, $value);
}
return $self->getParam(DEFAULTON);
}
=head2 type
Usage : $type = $filter->type();
Description: get filter type
Returntype : string
Exceptions : none
Caller : general
=cut
sub type {
my ($self) = @_;
return $self->getParam(TYPE);
}
=head2 filterCollection
Usage : $type = $filter->filterCollection();
Description: get filter collection filter belongs to
Returntype : reference to filter collection parent
Exceptions : none
Caller : general
=cut
sub filterCollection {
my ($self, $value) = @_;
if ($value){
$self->setParam(FILTERCOLLECTION, $value);
}
return $self->getParam(FILTERCOLLECTION);
}
=head2 setAttribute
Usage : Arg [1] - (optional) string $setAttribute
Description: get/set for set attribute
Returntype : string
Exceptions : none
Caller : general
=cut
sub setAttribute {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(SETATTRIBUTE, $value);
}
return $self->getParam(SETATTRIBUTE);
}
=head2 displayType
Usage : Arg [1] - (optional) string $displayType
Description: get/set for displayType
Returntype : string
Exceptions : none
Caller : general
=cut
sub displayType {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(DISPLAYTYPE, $value);
}
return $self->getParam(DISPLAYTYPE);
}
=head2 multipleValues
Usage : Arg [1] - (optional) string $multipleValues
Description: get/set for multipleValues
Returntype : string
Exceptions : none
Caller : general
=cut
sub multipleValues {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(MULTIPLEVALUES, $value);
}
return $self->getParam(MULTIPLEVALUES);
}
=head2 graph
Usage : Arg [1] - (optional) string $graph
Description: get/set for graph
Returntype : string
Exceptions : none
Caller : general
=cut
sub graph {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(GRAPH, $value);
}
return $self->getParam(GRAPH);
}
=head2 style
Usage : Arg [1] - (optional) string $style
Description: get/set for style
Returntype : string
Exceptions : none
Caller : general
=cut
sub style {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(STYLE, $value);
}
return $self->getParam(STYLE);
}
=head2 hideDisplay
Usage : Arg [1] - (optional) string $display
Description: get/set for style
Returntype : string
Exceptions : none
Caller : general
=cut
sub hideDisplay {
my ($self, $value) = @_;
if ($value){
$self->setParam(HIDEDISPLAY, $value);
}
return $self->getParam(HIDEDISPLAY);
}
=head2 legalQualifiers
Usage : Arg [1] - (optional) string $qualifiers
Description: get/set for legal_qualifiers
Returntype : string
Exceptions : none
Caller : general
=cut
sub legalQualifiers {
my ($self, $value) = @_;
if ($value){
$self->setParam(LEGAL_QUALIFIERS, $value);
}
return $self->getParam(LEGAL_QUALIFIERS);
}
=head2 autoCompletion
Usage : Arg [1] - (optional) string $autoCompletion
Description: get/set for autoCompletion
Returntype : string
Exceptions : none
Caller : general
=cut
sub autoCompletion {
# stores display name
my ($self, $value) = @_;
if ($value){
$self->setParam(AUTOCOMPLETION, $value);
}
return $self->getParam(AUTOCOMPLETION);
}
=head2 toSQL
Usage : my $sql = $filt->toSQL;
Description: Returns the SQL where clause reprensentation for a
particular BaseFilter implementation.
Returntype : SQL string
Exceptions : none
Caller : caller
=cut
sub toSQL {
my ($self,$oracle) = @_;
if ($self->can("_toSQL")) {
return $self->_toSQL($oracle);
}
$self->unimplemented_method;
}
sub _hashCode {
my $self = shift;
my $digest = Digest::MD5->new;
$digest->add($self->name) if ($self->name);
$digest->add($self->displayName) if ($self->displayName);
$digest->add($self->dataSetName) if ($self->dataSetName);
return $digest->hexdigest;
}
1;
]]>