Inheritance diagram for Bio::EnsEMBL::DBSQL::OntologyTermAdaptor:

Class Summary

Synopsis

  my $goa =
    $registry-\>get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );

  my $term = $goa-\>fetch_by_accession('GO:0010885');

  my @children    = @{ $goa-\>fetch_all_by_parent_term($term) };
  my @descendants = @{ $goa-\>fetch_all_by_ancestor_term($term) };

  my @parents   = @{ $goa-\>fetch_all_by_child_term($term) };
  my @ancestors = @{ $goa-\>fetch_all_by_descendant_term($term) };

  my %ancestor_chart = %{ $goa-\>_fetch_ancestor_chart($term) };

Description

An abstract adaptor class for fetching ontology
terms, creates Bio::EnsEMBL::OntologyTerm objects.

Definition at line 31 of file OntologyTermAdaptor.pm.

Available Methods
protected	_columns ()
protected	_default_where_clause ()
protected A	_fetch_ancestor_chart ()
protected	_fetch_synonyms_by_dbID ()
protected	_final_clause ()
protected	_left_join ()
protected	_list_dbIDs ()
protected	_objs_from_sth ()
protected	_straight_join ()
protected	_tables ()
public Listref	bind_param_generic_fetch ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public	dump_data ()
public	fetch_all ()
public Listref	fetch_all_by_ancestor_term ()
public Listref	fetch_all_by_child_term ()
public	fetch_all_by_dbID_list ()
public Listref	fetch_all_by_descendant_term ()
public Listref	fetch_all_by_name ()
public Listref	fetch_all_by_parent_term ()
public Bio::EnsEMBL::OntologyTerm	fetch_by_accession ()
public	fetch_by_dbID ()
public Listref	generic_fetch ()
public	get_dumped_data ()
public Boolean	is_multispecies ()
public Scalar	last_insert_id ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()
public DBI::StatementHandle	prepare ()
public Int	species_id ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_columns ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( ) [inherited]

Undocumented method

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.

protected A Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::_fetch_ancestor_chart ( )

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose ancestor terms should be fetched.

  Description   : Given a child ontology term, returns a hash
                  structure containing its ancestor terms, up to and
                  including any root term.  Relations of the type
                  'is_a' and 'part_of' are included.

  Example       :

    my %chart = %{ $ot_adaptor->_fetch_ancestor_chart($term) };

  Return type   : A reference to a hash structure like this:

    {
      'GO:XXXXXXX' => {
        'term' =>           # ref to Bio::EnsEMBL::OntologyTerm object
        'is_a'    => [...], # listref of Bio::EnsEMBL::OntologyTerm
        'part_of' => [...], # listref of Bio::EnsEMBL::OntologyTerm
      },
      'GO:YYYYYYY' => {
        # Similarly for all ancestors,
        # and including the query term itself.
      }
    }

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protected Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::_fetch_synonyms_by_dbID ( )

Undocumented method

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, and Bio::EnsEMBL::DBSQL::PredictionExonAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_left_join ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventAdaptor, Bio::EnsEMBL::DBSQL::TranscriptAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_objs_from_sth ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_tables ( ) [inherited]

Undocumented method

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public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::bind_param_generic_fetch ( ) [inherited]

 Arg [1]   : (optional)  scalar $param
              This is the parameter to bind
 Arg [2]   : (optional) int $sql_type
              Type of the parameter (from DBI (:sql_types))
 Example   :  $adaptor->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
              $adaptor->generic_fetch();
 Description:  When using parameters for the query, will call the bind_param to avoid
               some security issues. If there are no arguments, will return the bind_parameters
 ReturnType : listref
 Exceptions:  if called with one argument

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public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::db ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::BaseAdaptor::dbc ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBConnection $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBConnection
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_ancestor_term ( )

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose descendant terms should be fetched.

  Description   : Given a parent ontology term, returns a list of
                  all its descendant terms, down to and including
                  any leaf terms.  Relations of the type 'is_a' and
                  'part_of' are followed.

  Example       :

    my @descendants =
      @{ $ot_adaptor->fetch_all_by_ancestor_term($term) };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

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public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_child_term ( )

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose parent terms should be fetched.

  Description   : Given a child ontology term, returns a list of
                  its immediate parent terms.

  Example       :

    my @parents = @{ $ot_adaptor->fetch_all_by_child_term($term) };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

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public Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_dbID_list ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_descendant_term ( )

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose ancestor terms should be fetched.

  Arg [2]       : (optional) String
                  The subset within the ontolgy to which the query
                  should be restricted.  The subset may be specified as
                  a SQL pattern, e.g., "\%goslim\%" (but "goslim\%" might
                  not do what you expect), or as a specific subset name,
                  e.g., "goslim_generic".

  Arg [3]       : (optional) Boolean
                  If true (non-zero), only return the closest
                  term(s).  If this argument is true, and the
                  previous argument is left undefined, this method
                  will return the parent(s) of the given term.

  Description   : Given a child ontology term, returns a list of
                  all its ancestor terms, up to and including any
                  root term.  Relations of the type 'is_a' and
                  'part_of' are followed.  Optionally, only terms in
                  a given subset of the ontology may be returned,
                  and additionally one may ask to only get the
                  closest term(s) to the given child term.

  Example       :

    my @ancestors =
      @{ $ot_adaptor->fetch_all_by_descendant_term($term) };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

Code:

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sub fetch_all_by_descendant_term {
  my ( $this, $term, $subset, $closest_only ) = @_;

  assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );

  $closest_only ||= 0;

  my $statement = q(
SELECT DISTINCT
        parent_term.term_id,
        parent_term.accession,
        parent_term.name,
        parent_term.definition,
        parent_term.subsets,
        closure.distance
FROM    term parent_term
  JOIN  closure ON (closure.parent_term_id = parent_term.term_id)
WHERE   closure.child_term_id = ?
  AND   closure.distance > 0);

  if ( defined($subset) ) {
    if ( index( $subset, '%' ) != -1 ) {
      $statement .= q(
  AND   parent_term.subsets LIKE ?);
    } else {
      $statement .= q(
  AND   FIND_IN_SET(?, parent_term.subsets) > 0);
    }
  }

  $statement .= q(
ORDER BY closure.distance, parent_term.accession);

  my $sth = $this->prepare($statement);
  $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );

  if ( defined($subset) ) {
    $sth->bind_param( 2, $subset, SQL_VARCHAR );
  }

  $sth->execute();

  my ( $dbid, $accession, $name, $definition, $subsets, $distance );
  $sth->bind_columns(
      \( $dbid, $accession, $name, $definition, $subsets, $distance ) );

  my @terms;
  my $min_distance;

  while ( $sth->fetch() ) {
    $subsets ||= '';
    $min_distance ||= $distance;

    if ( !$closest_only || $distance == $min_distance ) {
      push( @terms,
            Bio::EnsEMBL::OntologyTerm->new(
                               '-dbid'      => $dbid,
                               '-adaptor'   => $this,
                               '-accession' => $accession,
                               '-ontology'  => $term->{'ontology'},
                               '-namespace' => $term->{'namespace'},
                               '-subsets' => [ split( /,/, $subsets ) ],
                               '-name'    => $name,
                               '-definition' => $definition, ) );
    } else {
      $sth->finish();
      last;
    }
  }

  return \@terms;
} ## end sub fetch_all_by_descendant_term

public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_name ( )

  Arg [1]       : String, name of term, or SQL pattern
  Arg [2]       : (optional) String, name of ontology

  Description   : Fetches ontology term(s) given a name, a synonym, or a
                  SQL pattern like "\%splice_site\%"

  Example       :

    my ($term) =
      @{ $ot_adaptor->fetch_by_name( 'DNA_binding_site', 'SO' ) };

    # Will find terms in both SO and GO:
    my @terms = @{ $ot_adaptor->fetch_by_name('%splice_site%') };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

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public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_parent_term ( )

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose children terms should be fetched.

  Description   : Given a parent ontology term, returns a list of
                  its immediate children terms.

  Example       :

    my @children =
      @{ $ot_adaptor->fetch_all_by_parent_term($term) };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

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public Bio::EnsEMBL::OntologyTerm Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_by_accession ( )

  Arg [1]       : String

  Description   : Fetches an ontology term given an accession.

  Example       :

    my $term = $ot_adaptor->fetch_by_accession('GO:0030326');

  Return type   : Bio::EnsEMBL::OntologyTerm

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public Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_by_dbID ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch ( ) [inherited]

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) Bio::EnsEMBL::AssemblyMapper $mapper
               A mapper object used to remap features
               as they are retrieved from the database
  Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice that features should be remapped to
  Example    : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
  Status     : Stable

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sub generic_fetch {
  my ($self, $constraint, $mapper, $slice) = @_;

  my @tabs = $self->_tables();

  my $extra_default_where;

  # Hack for feature types that needs to be restricted to species_id (in
  # coord_system).
  if (    $self->is_multispecies()
       && $self->isa('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor')
       && !$self->isa('Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor') )
  {
    # We do a check to see if there is already seq_region
    # and coord_system defined to ensure we get the right
    # alias.  We then do the extra query irrespectively of
    # what has already been specified by the user.
    my %thash = map { $_->[0] => $_->[1] } @tabs;

    my $sr_alias =
      ( exists( $thash{seq_region} ) ? $thash{seq_region} : 'sr' );
    my $cs_alias =
      ( exists( $thash{coord_system} ) ? $thash{coord_system} : 'cs' );

    if ( !exists( $thash{seq_region} ) ) {
      push( @tabs, [ 'seq_region', $sr_alias ] );
    }
    if ( !exists( $thash{coord_system} ) ) {
      push( @tabs, [ 'coord_system', $cs_alias ] );
    }

    $extra_default_where = sprintf(
                      '%s.seq_region_id = %s.seq_region_id '
                        . 'AND %s.coord_system_id = %s.coord_system_id '
                        . 'AND %s.species_id = ?',
                      $tabs[0]->[1], $sr_alias, $sr_alias,
                      $cs_alias,     $cs_alias );

    $self->bind_param_generic_fetch( $self->species_id(), SQL_INTEGER );
  } ## end if ( $self->is_multispecies...)

  my $columns = join(', ', $self->_columns());

  my $db = $self->db();

  #
  # Construct a left join statement if one was defined, and remove the
  # left-joined table from the table list
  #
  my @left_join_list = $self->_left_join();
  my $left_join_prefix = '';
  my $left_join = '';
  my @tables;
  if(@left_join_list) {
    my %left_join_hash = map { $_->[0] => $_->[1] } @left_join_list;
    while(my $t = shift @tabs) {
        my $t_alias = $t->[0] . " " . $t->[1];
      if( exists $left_join_hash{ $t->[0] } || exists $left_join_hash{$t_alias}) {
        my $condition = $left_join_hash{ $t->[0] };
        $condition ||= $left_join_hash{$t_alias};
        my $syn = $t->[1];
        $left_join .=
          "\n  LEFT JOIN " . $t->[0] . " $syn ON $condition ) ";
        $left_join_prefix .= '(';
      } else {
        push @tables, $t;
      }
    }
  } else {
    @tables = @tabs;
  }

  my $straight_join = '';

  if($self->_straight_join()) {
    $straight_join = "STRAIGHT_JOIN";
  }

  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

  my $sql =
      "SELECT $straight_join $columns\n"
    . "FROM $left_join_prefix ($tablenames) $left_join";

  my $default_where = $self->_default_where_clause();
  my $final_clause = $self->_final_clause;

  if ($extra_default_where) {
    if ($default_where) {
      $default_where .= "\n AND $extra_default_where";
    } else {
      $default_where = $extra_default_where;
    }
  }

  #append a where clause if it was defined
  if ($constraint) {
    $sql .= "\n WHERE $constraint ";
    if ($default_where) {
      $sql .= " AND\n       $default_where ";
    }
  } elsif ($default_where) {
    $sql .= "\n WHERE $default_where ";
  }

  #append additional clauses which may have been defined
  $sql .= "\n$final_clause";


  # FOR DEBUG:
  #printf(STDERR "SQL:\n%s\n", $sql);
  
  
  my $sth = $db->dbc->prepare($sql);
  my $bind_parameters = $self->bind_param_generic_fetch();
  if (defined $bind_parameters){
      #if we have bind the parameters, call the DBI to bind them
      my $i = 1;
      foreach my $param (@{$bind_parameters}){
        $sth->bind_param($i,$param->[0],$param->[1]);
        $i++;
      }
      #after binding parameters, undef for future queries
      $self->{'_bind_param_generic_fetch'} = ();
  }
  eval { $sth->execute() };
  if ($@) {
    throw("Detected an error whilst executing SQL '${sql}': $@");
  }

  my $res = $self->_objs_from_sth($sth, $mapper, $slice);
  $sth->finish();
  return $res;
}

Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.

public Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data ( ) [inherited]

Undocumented method

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public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::is_multispecies ( ) [inherited]

  Arg [1]    : (optional) boolean $arg
  Example    : if ($adaptor->is_multispecies()) { }
  Description: Getter/Setter for the is_multispecies boolean of
               to use for this adaptor.
  Returntype : boolean
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Scalar Bio::EnsEMBL::DBSQL::BaseAdaptor::last_insert_id ( ) [inherited]

  Arg [1]     : (optional) $field the name of the field the inserted ID was pushed 
                into
  Arg [2]     : (optional) HashRef used to pass extra attributes through to the 
                DBD driver
  Description : Delegating method which uses DBI to extract the last inserted 
                identifier. If using MySQL we just call the DBI method 
                DBI::last_insert_id() since MySQL ignores any extra
                arguments. See DBI for more information about this 
                delegated method. 
  Example     : my $id = $self->last_insert_id('my_id'); my $other_id = $self->last_insert_id();
  Returntype  : Scalar or undef

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public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::new ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection $dbobj
  Example    : $adaptor = new AdaptorInheritedFromBaseAdaptor($dbobj);
  Description: Creates a new BaseAdaptor object.  The intent is that this
               constructor would be called by an inherited superclass either
               automatically or through $self->SUPER::new in an overridden 
               new method.
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBConnection
  Status     : Stable

Code:

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public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare ( ) [inherited]

  Arg [1]    : string $string
               a SQL query to be prepared by this adaptors database
  Example    : $sth = $adaptor->prepare("select yadda from blabla")
  Description: provides a DBI statement handle from the adaptor. A convenience
               function so you dont have to write $adaptor->db->prepare all the
               time
  Returntype : DBI::StatementHandle
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::SliceAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id ( ) [inherited]

  Arg [1]    : (optional) int $species_id
               The internal ID of the species in a multi-species database.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the internal ID of the species in a
               multi-species database.  The default species ID is 1.
  Returntype : Integer
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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The documentation for this class was generated from the following file:

Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation