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Summary

BioMart::Configuration::ConfigurationTree

Package variables

Inherit

BioMart::Root

Synopsis

BioMart::Configuration::ConfigurationTree represent the whole of the
datasetConfig XML recovered from the mart database/server for a
particluar dataset

Description

BioMart::Configuration::ConfigurationTree is the top level object of
the object hierarchy representing the datasetConfig XML which describes
the attributes, filters available for each dataset.
The ConfigurationTree is a container for BioMart::Configuration::FilterTree
and BioMart::Configuration::AttributeTree objects.

Methods

Methods description

  Usage      : $ct->addAttributeTree($atree);
  Description: adds an AttributeTree to this ConfigurationTree. The
               order of addition of each AttributeTree is maintained.
  Returntype : na
  Exceptions : none
  Caller     : caller

  Usage      : $ct->addFilterTree($ag);
  Description: adds a FilterTree to this ConfigurationTree. The
               order of addition of each FilterTree is maintained.
  Returntype : na
  Exceptions : none
  Caller     : caller

  Usage        :  my $subName = $ct->dataSetName; $ct->dataSetName($newName);
  Description  :  Gets/Sets the name of the Dataset from which this 
                  ConfigurationTree originates.
  Returntype   :  scalar $name
  Exceptions   :  none
  Caller       :  caller

  Usage        :  my $subName = $ct->defaultDataset; 
                  $ct->defaultDataset($newName);
  Description  :  Gets/Sets the defaultDataset setting. If set to true
                  the the dataset using this configuration becomes the 
                  default.
  Returntype   :  scalar $defaultDataset
  Exceptions   :  none
  Caller       :  caller

  Usage        :  my $subName = $ct->entryLabel; 
                  $ct->entryLabel($newName);
  Description  :  Gets/Sets the entryLabel associated with this
                  configuration. 
  Returntype   :  entryLabel
  Exceptions   :  none
  Caller       :  caller

  Usage        :  my $subName = $ct->mart_Users; 
                  $ct->mart_Users($newName);
  Description  :  Gets/Sets the mart_Users associated with this
                  configuration. 
  Returntype   :  mart_Users comma separated list
  Exceptions   :  none
  Caller       :  caller

  Usage        :  my $subName = $ct->optionalParameters; 
                  $ct->optionalParameters($newName);
  Description  :  Gets/Sets the optionalParameters associated with this
                  configuration. Only used for GenomicSequence processing
                  at the moment.
  Returntype   :  scalar $optionalParameters
  Exceptions   :  none
  Caller       :  caller

  Usage        :  my $subName = $ct->primaryKeyRestriction; 
                  $ct->primaryKeyRestriction($newName);
  Description  :  Gets/Sets the primaryKeyRestriction associated with this
                  configuration. Can be used to restict data in the mart
                  available for querying by certain users
  Returntype   :  scalar $primaryKeyRestriction
  Exceptions   :  none
  Caller       :  caller

  Usage        :  my $subName = $ct->software_version; 
                  $ct->software_version($newName);
  Description  :  Gets/Sets the software_version associated with this
                  configuration. 
  Returntype   :  software_version
  Exceptions   :  none
  Caller       :  caller

  Usage        :  my $subName = $ct->visibleFilterPage; 
                  $ct->visibleFilterPage($newName);
  Description  :  Gets/Sets the visibleFilterPage associated with this
                  configuration.
  Returntype   :  scalar $visibleFilterPage
  Exceptions   :  none
  Caller       :  caller

Methods code

sub _new {

  my ($self, @param) = @_;

  $self->SUPER::_new(@param);

  $self->addParams(TITLES, @param);

  $self->attr('attTs', []);
  $self->attr('filtTs', []);
  $self->attr(OPTPARAM, undef);
  $self->attr(RESTRICTEDPARAM, undef);
  $self->attr(DEFDATASET, undef);
  $self->attr(VISIBLEFILTERPAGE, undef);
  $self->attr(MARTUSERS, 'default');
  $self->attr(SOFTWAREVERSION, undef);
  $self->attr(ENTRYLABEL, undef);

}

sub addAttributeTree {

  my ($self, $attTree) = @_;

  my $attTs = $self->get('attTs');
  push @{$attTs}, $attTree;

}

sub addFilterTree {

  my ($self, $filtTree) = @_;

  my $filtTs = $self->get('filtTs');
  push @{$filtTs}, $filtTree;

}

sub dataSetName {

  my ($self, $name) = @_;

  if ($name) {
    $self->setParam(DATASETNAME, $name);
  }

  return $self->getParam(DATASETNAME);

}

sub defaultDataset {

  my ($self, $param) = @_;
  if ($param) {
    $self->set(DEFDATASET, $param);
  }
  return $self->get(DEFDATASET);

}

sub entryLabel {

  my ($self, $param) = @_;
  if ($param) {
    $self->set(ENTRYLABEL, $param);
  }
  return $self->get(ENTRYLABEL);

}

sub getAllAttributeTrees {

  my $self = shift;

  return $self->get('attTs');

}

sub getAllFilterTrees {

  my $self = shift;

  return $self->get('filtTs');

}

sub getAttributeByName {

  my ($self, $name) = @_;

  my $retAtt;

  my $attTs = $self->get('attTs');
  foreach my $attT (@{$attTs}) {
    $retAtt = $attT->getAttributeByName($name);
    last if ($retAtt);
  }

  return $retAtt;

}

sub getAttributeByNameKey {

  my ($self, $name, $key) = @_;

  my $retAtt;

  my $attTs = $self->get('attTs');
  foreach my $attT (@{$attTs}) {
    $retAtt = $attT->getAttributeByNameKey($name,$key);
    last if ($retAtt);
  }

  return $retAtt;

}

sub getAttributeTreeByName {

  my ($self, $name) = @_;

  my $retTree;

  my $attTs = $self->get('attTs');

  foreach my $attT (@{$attTs}) {
    if (($attT->name() && $name) && $attT->name() eq $name) {
      $retTree = $attT;
      last;
	}
  }

  return $retTree;

}

sub getFilterByName {

  my ($self, $name) = @_;

  my $retFilt;

  my $filtTs = $self->get('filtTs');
  foreach my $filtT (@{$filtTs}) {
    $retFilt = $filtT->getFilterByName($name);
  
    unless ($retFilt) {
	#then try option
	my $opt = $filtT->getOptionByName($name);
	if ($opt) {
	    $retFilt = $opt->filter;
	}
    }
    last if ($retFilt);
  }

  return $retFilt if ($retFilt);
  # if not found may be a filter in an attributePage
  my $attTs = $self->get('attTs');
  foreach my $attT (@{$attTs}) {
    my $potFilt = $attT->getFilterByName($name);
    if ($potFilt && $potFilt->isa("BioMart::Configuration::ValueFilter")){
	$retFilt = $potFilt;
	last;
    }
  }

  return $retFilt;

}

sub getFilterTreeByName {

  my ($self, $name) = @_;

  my $retTree;

  my $filtTs = $self->get('filtTs');

  foreach my $filtT (@{$filtTs}) {
    if ($filtT->name() eq $name) {
      $retTree = $filtT;
      last;
	}
  }

  return $retTree;

}

sub getOptionByName {

  my ($self, $name) = @_;

  my $retOption;

  my $filtTs = $self->get('filtTs');
  foreach my $filtT (@{$filtTs}) {
    $retOption = $filtT->getOptionByName($name);
    last if ($retOption);
  }

  return $retOption;

}

sub mart_Users {

  my ($self, $param) = @_;
  if ($param) {
    $self->set(MARTUSERS, $param);
  }
  return $self->get(MARTUSERS);

}

sub optionalParameters {

  my ($self, $param) = @_;
  if ($param) {
    $self->set(OPTPARAM, $param);
  }
  return $self->get(OPTPARAM);

}

sub primaryKeyRestriction {

  my ($self, $param) = @_;
  if ($param) {
    $self->set(RESTRICTEDPARAM, $param);
  }
  return $self->get(RESTRICTEDPARAM);

}

sub software_version {

  my ($self, $param) = @_;
  if ($param) {
    $self->set(SOFTWAREVERSION, $param);
  }
  return $self->get(SOFTWAREVERSION);

}

sub toXML {

  my ($self, $xml) = @_;

  if ($xml) {
     $self->{'datasetConfigXML'}=$xml;
  }
  return $self->{'datasetConfigXML'};
}






1;

}

sub visibleFilterPage {

  my ($self, $param) = @_;
  if ($param) {
    $self->set(VISIBLEFILTERPAGE, $param);
  }
  return $self->get(VISIBLEFILTERPAGE);

}

General documentation

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