BioMart::Configuration BaseFilter
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Summary
BioMart::Configuration::BaseFilter
Package variables
No package variables defined.
Included modules
Digest::MD5
Inherit
BioMart::Root
Synopsis
Base Interface for all BioMart filters.
Description
Base Interface for BioMart filters
Methods
_hashCode
No description
Code
_init
No description
Code
_newDescriptionCode
addDependencyDescriptionCode
addOptionDescriptionCode
addOptionsDescriptionCode
autoCompletionDescriptionCode
buttonURLDescriptionCode
dataSetNameDescriptionCode
defaultOnDescriptionCode
dependenciesDescriptionCode
dependsOnDescriptionCode
dependsOnTypeDescriptionCode
descriptionDescriptionCode
displayNameDescriptionCode
displayTypeDescriptionCode
filterCollectionDescriptionCode
getAllOptionsDescriptionCode
graphDescriptionCode
hideDisplayDescriptionCode
imageURLDescriptionCode
interfaceDescriptionCode
legalQualifiersDescriptionCode
multipleValuesDescriptionCode
nameDescriptionCode
pointedFromDatasetDescriptionCode
pointedFromInterfaceDescriptionCode
setAttributeDescriptionCode
setAttributePageDescriptionCode
styleDescriptionCode
tableDescriptionCode
toSQLDescriptionCode
typeDescriptionCode
Methods description
_newcode    nextTop
  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
addDependencycodeprevnextTop
  Usage      : usage
  Description: Description
  Returntype : 
  Exceptions : none
  Caller     : caller
addOptioncodeprevnextTop
  Usage      : usage
  Description: Description
  Returntype : 
  Exceptions : none
  Caller     : caller
addOptionscodeprevnextTop
  Usage      : usage
  Description: Description
  Returntype : 
  Exceptions : none
  Caller     : caller
autoCompletioncodeprevnextTop
  Usage      : Arg [1] - (optional) string $autoCompletion
  Description: get/set for autoCompletion
  Returntype : string
  Exceptions : none
  Caller     : general
buttonURLcodeprevnextTop
  Usage      : Arg [1] - (optional) string $buttonURL
  Description: get/set for display name
  Returntype : string
  Exceptions : none
  Caller     : general
dataSetNamecodeprevnextTop
  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
defaultOncodeprevnextTop
  Usage      : Arg [1] - (optional) string $defaultOn
  Description: get/set for default on
  Returntype : string
  Exceptions : none
  Caller     : general
dependenciescodeprevnextTop
  Usage      : usage
  Description: Description
  Returntype :
  Exceptions : none
  Caller     : caller
dependsOncodeprevnextTop
  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
dependsOnTypecodeprevnextTop
  Usage      : Arg [1] - (optional) string $dependsOnType
  Description: get/set for dependsOnType - all or any are acceptable.
  Returntype : string
  Exceptions : none
  Caller     : general
descriptioncodeprevnextTop
  Usage      : Arg [1] - (optional) string $description
  Description: get/set for description
  Returntype : string
  Exceptions : none
  Caller     : general
displayNamecodeprevnextTop
  Usage      : Arg [1] - (optional) string $display_name
  Description: get/set for display name
  Returntype : string
  Exceptions : none
  Caller     : general
displayTypecodeprevnextTop
  Usage      : Arg [1] - (optional) string $displayType
  Description: get/set for displayType
  Returntype : string
  Exceptions : none
  Caller     : general
filterCollectioncodeprevnextTop
  Usage      : $type = $filter->filterCollection();
  Description: get filter collection filter belongs to
  Returntype : reference to filter collection parent
  Exceptions : none
  Caller     : general
getAllOptionscodeprevnextTop
  Usage      : usage
  Description: Description
  Returntype :
  Exceptions : none
  Caller     : caller
graphcodeprevnextTop
  Usage      : Arg [1] - (optional) string $graph
  Description: get/set for graph
  Returntype : string
  Exceptions : none
  Caller     : general
hideDisplaycodeprevnextTop
  Usage      : Arg [1] - (optional) string $display
  Description: get/set for style
  Returntype : string
  Exceptions : none
  Caller     : general
imageURLcodeprevnextTop
  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
interfacecodeprevnextTop
  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
legalQualifierscodeprevnextTop
  Usage      : Arg [1] - (optional) string $qualifiers
  Description: get/set for legal_qualifiers
  Returntype : string
  Exceptions : none
  Caller     : general
multipleValuescodeprevnextTop
  Usage      : Arg [1] - (optional) string $multipleValues
  Description: get/set for multipleValues
  Returntype : string
  Exceptions : none
  Caller     : general
namecodeprevnextTop
  Usage      : my $name = $filt->name; $filt->name($newName);
  Description: get/set for the name of the filter
  Returntype : scalar $name
  Exceptions : none
  Caller     : caller
pointedFromDatasetcodeprevnextTop
  Usage      : Arg [1] - (optional) string $pointedFromDataset
  Description: get/set for pointedFromDataset atribute(s) for a dataset
  Returntype : string
  Exceptions : none
  Caller     : general
pointedFromInterfacecodeprevnextTop
  Usage      : Arg [1] - (optional) string $pointedFromInterface
  Description: get/set for pointedFromInterface atribute(s) for a dataset
  Returntype : string
  Exceptions : none
  Caller     : general
setAttributecodeprevnextTop
  Usage      : Arg [1] - (optional) string $setAttribute
  Description: get/set for set attribute
  Returntype : string
  Exceptions : none
  Caller     : general
setAttributePagecodeprevnextTop
  Usage      : Arg [1] - (optional) string $setAttributePage
  Description: get/set for display name
  Returntype : string
  Exceptions : none
  Caller     : general
stylecodeprevnextTop
  Usage      : Arg [1] - (optional) string $style
  Description: get/set for style
  Returntype : string
  Exceptions : none
  Caller     : general
tablecodeprevnextTop
  Usage      :
  Description: returns the table name associated with this filter;
  Returntype : String table name
  Exceptions : none
  Caller     : caller
toSQLcodeprevnextTop
  Usage      : my $sql = $filt->toSQL;
  Description: Returns the SQL where clause reprensentation for a 
               particular BaseFilter implementation.
  Returntype : SQL string
  Exceptions : none
  Caller     : caller
typecodeprevnextTop
  Usage      : $type = $filter->type();
  Description: get filter type
  Returntype : string
  Exceptions : none
  Caller     : general
Methods code
_hashCodedescriptionprevnextTop
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;
}
_initdescriptionprevnextTop
sub _init {
  my ($self, @param) = @_;
  $self->SUPER::_init(@param);
  my $proto = shift @param;
  $self->attr('options', $proto->getAllOptions);
}
_newdescriptionprevnextTop
sub _new {
  my ($self, @param) = @_;
  $self->SUPER::_new(@param);
  $self->addParams(TITLES, @param);
  $self->attr('options', []);
	$self->attr('dependency',[]);
}
addDependencydescriptionprevnextTop
sub addDependency {
  my ($self, $resolvedDependency) = @_;

  push @{$self->get('dependency')}, $resolvedDependency;
}
addOptiondescriptionprevnextTop
sub addOption {
  my ($self, $option) = @_;
  my $options = $self->get('options');
  push @{$options}, $option;
}
addOptionsdescriptionprevnextTop
sub addOptions {
  my ($self, $new_options) = @_;
  my $options = $self->get('options');
  push @{$options}, @{$new_options};
}
autoCompletiondescriptionprevnextTop
sub autoCompletion {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(AUTOCOMPLETION, $value);
  }
  return $self->getParam(AUTOCOMPLETION);
}
buttonURLdescriptionprevnextTop
sub buttonURL {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(BUTTONURL, $value);
  }
  return $self->getParam(BUTTONURL);
}
dataSetNamedescriptionprevnextTop
sub dataSetName {
  my ($self, $name) = @_;

  if ($name) {
    $self->setParam(DATASETNAME, $name);
  }
  return $self->getParam(DATASETNAME);
}
defaultOndescriptionprevnextTop
sub defaultOn {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(DEFAULTON, $value);
  }
  return $self->getParam(DEFAULTON);
}
dependenciesdescriptionprevnextTop
sub dependencies {
  my $self = shift;

  return $self->get('dependency');
}
dependsOndescriptionprevnextTop
sub dependsOn {
  my ($self, $value) = @_;
  
  if ($value){
    $self->setParam(DEPENDSON, $value);
  }
  return $self->getParam(DEPENDSON);
}
dependsOnTypedescriptionprevnextTop
sub dependsOnType {
  my ($self, $value) = @_;
  
  if ($value){
    $self->setParam(DEPENDSONTYPE, $value);
  }
  return $self->getParam(DEPENDSONTYPE);
}
descriptiondescriptionprevnextTop
sub description {
  # stores description
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(DESCRIPTION, $value);
  }
  return $self->getParam(DESCRIPTION);
}
displayNamedescriptionprevnextTop
sub displayName {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(DISPLAYNAME, $value);
  }
  return $self->getParam(DISPLAYNAME);
}
displayTypedescriptionprevnextTop
sub displayType {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(DISPLAYTYPE, $value);
  }
  return $self->getParam(DISPLAYTYPE);
}
filterCollectiondescriptionprevnextTop
sub filterCollection {
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(FILTERCOLLECTION, $value);
  }

  return $self->getParam(FILTERCOLLECTION);
}
getAllOptionsdescriptionprevnextTop
sub getAllOptions {
  my $self = shift;
  return $self->get('options');
}
graphdescriptionprevnextTop
sub graph {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(GRAPH, $value);
  }
  return $self->getParam(GRAPH);
}
hideDisplaydescriptionprevnextTop
sub hideDisplay {
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(HIDEDISPLAY, $value);
  }
  return $self->getParam(HIDEDISPLAY);
}
imageURLdescriptionprevnextTop
sub imageURL {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(IMAGEURL, $value);
  }
  return $self->getParam(IMAGEURL);
}
interfacedescriptionprevnextTop
sub interface {
  my ($self, $value) = @_;
  if ($value){
      $self->setParam(INTERFACE, $value);
  }
  return $self->getParam(INTERFACE);
}
legalQualifiersdescriptionprevnextTop
sub legalQualifiers {
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(LEGAL_QUALIFIERS, $value);
  }
  return $self->getParam(LEGAL_QUALIFIERS);
}
multipleValuesdescriptionprevnextTop
sub multipleValues {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(MULTIPLEVALUES, $value);
  }
  return $self->getParam(MULTIPLEVALUES);
}
namedescriptionprevnextTop
sub name {
  my ($self, $value) = @_;
  if ($value){
      $self->setParam(NAME, $value);
  }
  return $self->getParam(NAME);
}
pointedFromDatasetdescriptionprevnextTop
sub pointedFromDataset {
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(POINTEDFROMDATASET, $value);
  }
  return $self->getParam(POINTEDFROMDATASET);
}
pointedFromInterfacedescriptionprevnextTop
sub pointedFromInterface {
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(POINTEDFROMINTERFACE, $value);
  }
  return $self->getParam(POINTEDFROMINTERFACE);
}
setAttributedescriptionprevnextTop
sub setAttribute {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(SETATTRIBUTE, $value);
  }
  return $self->getParam(SETATTRIBUTE);
}
setAttributePagedescriptionprevnextTop
sub setAttributePage {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(SETATTRIBUTEPAGE, $value);
  }
  return $self->getParam(SETATTRIBUTEPAGE);
}
styledescriptionprevnextTop
sub style {
  # stores display name
  my ($self, $value) = @_;
  if ($value){
    $self->setParam(STYLE, $value);
  }
  return $self->getParam(STYLE);
}
tabledescriptionprevnextTop
sub table {
  #my $self = shift;
  #my $attribute = $self->get('attribute');
  #return $attribute->table;
return "";
}
toSQLdescriptionprevnextTop
sub toSQL {
  my ($self,$oracle) = @_;

  if ($self->can("_toSQL")) {
    return $self->_toSQL($oracle);
  }
  $self->unimplemented_method;
}
typedescriptionprevnextTop
sub type {
  my ($self) = @_;
  return $self->getParam(TYPE);
}
General documentation
AUTHOR - Arek Kasprzyk, Syed Haider, Richard Holland, Darin London, Damian SmedleyTop
CONTACTTop
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