Inheritance diagram for Bio::EnsEMBL::DBSQL::OperonAdaptor:

Class Summary

Synopsis

my $operon_adaptor =  Bio::EnsEMBL::DBSQL::OperonAdaptor-\>new($dba);
$operon_adaptor-\>store($operon);
my $operon2 = $operon_adaptor-\>fetch_by_dbID( $operon-\>dbID() );

Description

This is a database aware adaptor for the retrieval and storage of operon
objects.

Definition at line 24 of file OperonAdaptor.pm.

Available Methods
protected	_check_start_end_strand ()
protected	_columns ()
protected	_create_feature ()
protected	_create_feature_fast ()
protected	_default_where_clause ()
protected	_final_clause ()
protected	_left_join ()
protected	_list_dbIDs ()
protected	_list_seq_region_ids ()
protected	_logic_name_to_constraint ()
protected	_max_feature_length ()
protected	_objs_from_sth ()
protected	_pre_store ()
protected	_pre_store_userdata ()
protected	_remap ()
protected Bio::EnsEMBL::Utils::Cache	_slice_feature_cache ()
protected	_slice_fetch ()
protected	_straight_join ()
protected	_tables ()
public Listref	bind_param_generic_fetch ()
public void	clear_cache ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public	dump_data ()
public Listref	fetch_all ()
public Listref	fetch_all_by_dbID_list ()
public Listref	fetch_all_by_logic_name ()
public	fetch_all_by_RawContig ()
public	fetch_all_by_RawContig_and_score ()
public	fetch_all_by_RawContig_constraint ()
public Reference	fetch_all_by_Slice ()
public Listref	fetch_all_by_Slice_and_score ()
public Listref	fetch_all_by_Slice_constraint ()
public Listref	fetch_all_versions_by_stable_id ()
public Bio::EnsEMBL::Feature	fetch_by_dbID ()
public Bio::EnsEMBL::Operon	fetch_by_name ()
public	fetch_by_operon_transcript ()
public	fetch_by_operon_transcript_id ()
public Bio::EnsEMBL::Operon	fetch_by_operon_transcript_stable_id ()
public Bio::EnsEMBL::Operon	fetch_by_stable_id ()
public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice ()
public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice_method ()
public Listref	generic_fetch ()
public	get_dumped_data ()
public	get_seq_region_id_external ()
public	get_seq_region_id_internal ()
public Boolean	is_multispecies ()
public Scalar	last_insert_id ()
public Listref	list_dbIDs ()
public	list_seq_region_ids ()
public Reference	list_stable_ids ()
public Bio::EnsEMBL::BaseFeatureAdaptor	new ()
public DBI::StatementHandle	prepare ()
public void	remove ()
public	remove_by_analysis_id ()
public	remove_by_feature_id ()
public	remove_by_RawContig ()
public void	remove_by_Slice ()
public Int	species_id ()
public Boolean	start_equals_end ()
public The	store ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_check_start_end_strand ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::OperonAdaptor::_columns ( )

Undocumented method

Code:

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

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_create_feature ( ) [inherited]

Undocumented method

Code:

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

Undocumented method

Code:

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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

Code:

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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

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_list_seq_region_ids ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_logic_name_to_constraint ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_max_feature_length ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::OperonAdaptor::_objs_from_sth ( )

Undocumented method

Code:

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sub _objs_from_sth {
    my ( $self, $sth, $mapper, $dest_slice ) = @_;

    #
    # This code is ugly because an attempt has been made to remove as many
    # function calls as possible for speed purposes.  Thus many caches and
    # a fair bit of gymnastics is used.
    #

    my $sa = $self->db()->get_SliceAdaptor();
    my $aa = $self->db->get_AnalysisAdaptor();

    my @operons;
    my %analysis_hash;
    my %slice_hash;
    my %sr_name_hash;
    my %sr_cs_hash;
    my ( $stable_id, $version, $created_date, $modified_date, $analysis_id );

    my ( $operon_id,      $seq_region_id,     $seq_region_start,
         $seq_region_end, $seq_region_strand, $display_label );

    $sth->bind_columns( \$operon_id,         \$seq_region_id,
                        \$seq_region_start,  \$seq_region_end,
                        \$seq_region_strand, \$display_label,
                        \$analysis_id,       \$stable_id,
                        \$version,           \$created_date,
                        \$modified_date );

    my $asm_cs;
    my $cmp_cs;
    my $asm_cs_vers;
    my $asm_cs_name;
    my $cmp_cs_vers;
    my $cmp_cs_name;
    if ($mapper) {
        $asm_cs      = $mapper->assembled_CoordSystem();
        $cmp_cs      = $mapper->component_CoordSystem();
        $asm_cs_name = $asm_cs->name();
        $asm_cs_vers = $asm_cs->version();
        $cmp_cs_name = $cmp_cs->name();
        $cmp_cs_vers = $cmp_cs->version();
    }

    my $dest_slice_start;
    my $dest_slice_end;
    my $dest_slice_strand;
    my $dest_slice_length;
    my $dest_slice_sr_name;
    my $dest_slice_seq_region_id;
    if ($dest_slice) {
        $dest_slice_start         = $dest_slice->start();
        $dest_slice_end           = $dest_slice->end();
        $dest_slice_strand        = $dest_slice->strand();
        $dest_slice_length        = $dest_slice->length();
        $dest_slice_sr_name       = $dest_slice->seq_region_name();
        $dest_slice_seq_region_id = $dest_slice->get_seq_region_id();
    }

    my $count = 0;
  OPERON: while ( $sth->fetch() ) {
        $count++;
        #get the analysis object
        my $analysis = $analysis_hash{$analysis_id} ||=
          $aa->fetch_by_dbID($analysis_id);
        $analysis_hash{$analysis_id} = $analysis;
        #need to get the internal_seq_region, if present
        $seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
        #get the slice object
        my $slice = $slice_hash{ "ID:" . $seq_region_id };

        if ( !$slice ) {
            $slice = $sa->fetch_by_seq_region_id($seq_region_id);
            $slice_hash{ "ID:" . $seq_region_id } = $slice;
            $sr_name_hash{$seq_region_id}         = $slice->seq_region_name();
            $sr_cs_hash{$seq_region_id}           = $slice->coord_system();
        }

        my $sr_name = $sr_name_hash{$seq_region_id};
        my $sr_cs   = $sr_cs_hash{$seq_region_id};
        #
        # remap the feature coordinates to another coord system
        # if a mapper was provided
        #
        if ($mapper) {

            (  $seq_region_id,  $seq_region_start,
               $seq_region_end, $seq_region_strand )
              = $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
                                  $seq_region_strand, $sr_cs );

            #skip features that map to gaps or coord system boundaries
            next OPERON if ( !defined($seq_region_id) );

            #get a slice in the coord system we just mapped to
            if ( $asm_cs == $sr_cs
                 || ( $cmp_cs != $sr_cs && $asm_cs->equals($sr_cs) ) )
            {
                $slice = $slice_hash{ "ID:" . $seq_region_id } ||=
                  $sa->fetch_by_seq_region_id($seq_region_id);
            } else {
                $slice = $slice_hash{ "ID:" . $seq_region_id } ||=
                  $sa->fetch_by_seq_region_id($seq_region_id);
            }
        }

       #
       # If a destination slice was provided convert the coords
       # If the dest_slice starts at 1 and is foward strand, nothing needs doing
       #
        if ($dest_slice) {
            if ( $dest_slice_start != 1 || $dest_slice_strand != 1 ) {
                if ( $dest_slice_strand == 1 ) {
                    $seq_region_start =
                      $seq_region_start - $dest_slice_start + 1;
                    $seq_region_end = $seq_region_end - $dest_slice_start + 1;
                } else {
                    my $tmp_seq_region_start = $seq_region_start;
                    $seq_region_start = $dest_slice_end - $seq_region_end + 1;
                    $seq_region_end =
                      $dest_slice_end - $tmp_seq_region_start + 1;
                    $seq_region_strand *= -1;
                }
            }

            #throw away features off the end of the requested slice
            if (    $seq_region_end < 1
                 || $seq_region_start > $dest_slice_length
                 || ( $dest_slice_seq_region_id != $seq_region_id ) )
            {
#   print STDERR "IGNORED DUE TO CUTOFF  $dest_slice_seq_region_id ne $seq_region_id . $sr_name\n";
                next OPERON;
            }
            $slice = $dest_slice;
        } ## end if ($dest_slice)

        push( @operons,
              Bio::EnsEMBL::Operon->new(
                                      -START         => $seq_region_start,
                                      -END           => $seq_region_end,
                                      -STRAND        => $seq_region_strand,
                                      -SLICE         => $slice,
                                      -DISPLAY_LABEL => $display_label,
                                      -ADAPTOR       => $self,
                                      -DBID          => $operon_id,
                                      -STABLE_ID     => $stable_id,
                                      -VERSION       => $version,
                                      -CREATED_DATE  => $created_date || undef,
                                      -MODIFIED_DATE => $modified_date || undef,
                                      -ANALYSIS      => $analysis ) );

    } ## end while ( $sth->fetch() )

    return \@operons;
} ## end sub _objs_from_sth

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

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_pre_store ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_pre_store_userdata ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_remap ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Utils::Cache Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_feature_cache ( ) [inherited]

 
  Description	: Returns the feature cache if we are allowed to cache and
                will build it if we need to. We will never return a reference
                to the hash to avoid unintentional auto-vivfying caching
  Returntype 	: Bio::EnsEMBL::Utils::Cache
  Exceptions 	: None
  Caller     	: Internal

Code:

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protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_fetch ( ) [inherited]

Undocumented method

Code:

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sub _slice_fetch {
  my ( $self, $slice, $orig_constraint ) = @_;

  my $slice_start         = $slice->start();
  my $slice_end           = $slice->end();
  my $slice_strand        = $slice->strand();
  my $slice_cs            = $slice->coord_system();
  my $slice_seq_region    = $slice->seq_region_name();
  my $slice_seq_region_id = $slice->get_seq_region_id();

  #get the synonym and name of the primary_table
  my @tabs = $self->_tables;
  my ( $tab_name, $tab_syn ) = @{ $tabs[0] };

  #find out what coordinate systems the features are in
  my $mcc      = $self->db->get_MetaCoordContainer();
  my @feat_css = ();

  my $mca        = $self->db->get_MetaContainer();
  my $value_list = $mca->list_value_by_key( $tab_name . "build.level" );
  if ( @$value_list and $slice->is_toplevel() ) {
    push @feat_css, $slice_cs;
  } else {
    @feat_css =
      @{ $mcc->fetch_all_CoordSystems_by_feature_type($tab_name) };
  }

  my $asma = $self->db->get_AssemblyMapperAdaptor();
  my @features;

  # fetch the features from each coordinate system they are stored in
COORD_SYSTEM: foreach my $feat_cs (@feat_css) {
    my $mapper;
    my @coords;
    my @ids;

    if ( $feat_cs->equals($slice_cs) ) {
      # no mapping is required if this is the same coord system

      my $max_len = $self->_max_feature_length()
        || $mcc->fetch_max_length_by_CoordSystem_feature_type( $feat_cs,
                                                            $tab_name );

      my $constraint = $orig_constraint;

      my $sr_id;
      if ( $slice->adaptor() ) {
        $sr_id = $slice->adaptor()->get_seq_region_id($slice);
      } else {
        $sr_id =
          $self->db()->get_SliceAdaptor()->get_seq_region_id($slice);
      }

      # If there is mapping information, use the external_seq_region_id
      # to get features.

      my @sr_ids = ($sr_id);

      while (1) {
        my $ext_sr_id = $self->get_seq_region_id_external($sr_id);

        if ( $ext_sr_id == $sr_id ) { last }

        push( @sr_ids, $ext_sr_id );
        $sr_id = $ext_sr_id;
      }

      $constraint .= " AND " if ($constraint);

      
      $constraint .= "${tab_syn}.seq_region_id IN ("
          . join( ',', @sr_ids ) . ") AND";

      #faster query for 1bp slices where SNP data is not compressed
      if ( $self->start_equals_end && $slice_start == $slice_end ) {
      $constraint .=
          " AND ${tab_syn}.seq_region_start = $slice_end" .
          " AND ${tab_syn}.seq_region_end = $slice_start";

      } else {

      if ( !$slice->is_circular() ) {
          # Deal with the default case of a non-circular chromosome.
          $constraint .= " ${tab_syn}.seq_region_start <= $slice_end AND "
          . "${tab_syn}.seq_region_end >= $slice_start";

          if ( $max_len ) {
          my $min_start = $slice_start - $max_len;
          $constraint .= " AND ${tab_syn}.seq_region_start >= $min_start";
          }

      } else {
          # Deal with the case of a circular chromosome.
          if ( $slice_start > $slice_end ) {
          $constraint .= " ( ${tab_syn}.seq_region_start >= $slice_start "
              . "OR ${tab_syn}.seq_region_start <= $slice_end "
              . "OR ${tab_syn}.seq_region_end >= $slice_start "
              . "OR ${tab_syn}.seq_region_end <= $slice_end "
              . "OR ${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end)";

          } else {
          $constraint .= " ((${tab_syn}.seq_region_start <= $slice_end "
              . "AND ${tab_syn}.seq_region_end >= $slice_start) "
              . "OR (${tab_syn}.seq_region_start > ${tab_syn}.seq_region_end "
              . "AND (${tab_syn}.seq_region_start <= $slice_end "
              . "OR ${tab_syn}.seq_region_end >= $slice_start)))";
          }
      }

      }

      my $fs = $self->generic_fetch( $constraint, undef, $slice );

    # features may still have to have coordinates made relative to slice
    # start
      $fs = $self->_remap( $fs, $mapper, $slice );

      push @features, @$fs;
    } else {
      $mapper = $asma->fetch_by_CoordSystems( $slice_cs, $feat_cs );

      next unless defined $mapper;

      # Get list of coordinates and corresponding internal ids for
      # regions the slice spans
      @coords =
        $mapper->map( $slice_seq_region, $slice_start, $slice_end,
                      $slice_strand, $slice_cs );

      @coords = grep { !$_->isa('Bio::EnsEMBL::Mapper::Gap') } @coords;

      next COORD_SYSTEM if ( !@coords );

      @ids = map { $_->id() } @coords;
      #coords are now id rather than name
      #      @ids = @{$asma->seq_regions_to_ids($feat_cs, \@ids)};

      # When regions are large and only partially spanned
      # by slice it is faster to to limit the query with
      # start and end constraints.  Take simple approach:
      # use regional constraints if there are less than a
      # specific number of regions covered.

      if ( @coords > $MAX_SPLIT_QUERY_SEQ_REGIONS ) {
        my $constraint = $orig_constraint;
        my $id_str = join( ',', @ids );
        $constraint .= " AND " if ($constraint);
        $constraint .= "${tab_syn}.seq_region_id IN ($id_str)";
        my $fs = $self->generic_fetch( $constraint, $mapper, $slice );

        $fs = $self->_remap( $fs, $mapper, $slice );

        push @features, @$fs;

      } else {
        # do multiple split queries using start / end constraints

        my $max_len = (
                $self->_max_feature_length()
                  || $mcc->fetch_max_length_by_CoordSystem_feature_type(
                                                     $feat_cs, $tab_name
                  ) );

        my $len = @coords;
        for ( my $i = 0; $i < $len; $i++ ) {
          my $constraint = $orig_constraint;
          $constraint .= " AND " if ($constraint);
          $constraint .=
              "${tab_syn}.seq_region_id = "
            . $ids[$i] . " AND "
            . "${tab_syn}.seq_region_start <= "
            . $coords[$i]->end() . " AND "
            . "${tab_syn}.seq_region_end >= "
            . $coords[$i]->start();

          if ($max_len) {
            my $min_start = $coords[$i]->start() - $max_len;
            $constraint .=
              " AND ${tab_syn}.seq_region_start >= $min_start";
          }
          my $fs = $self->generic_fetch( $constraint, $mapper, $slice );

          $fs = $self->_remap( $fs, $mapper, $slice );

          push @features, @$fs;
        }
      } ## end else [ if ( @coords > $MAX_SPLIT_QUERY_SEQ_REGIONS)]
    } ## end else [ if ( $feat_cs->equals(...))]
  } ## end foreach my $feat_cs (@feat_css)

  return \@features;
} ## end sub _slice_fetch

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

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::OperonAdaptor::_tables ( )

Undocumented method

Code:

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

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

Code:

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public void Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::clear_cache ( ) [inherited]

  Args      : None
  Example   : my $sa =
                $registry->get_adaptor( 'Mus musculus', 'Core',
                                        'Slice' );
              my $ga =
                $registry->get_adaptor( 'Mus musculus', 'Core',
                                        'Gene' );

              my $slice =
                $sa->fetch_by_region( 'Chromosome', '1', 1e8,
                                      1.05e8 );

              my $genes = $ga->fetch_all_by_Slice($slice);

              $ga->clear_cache();

  Description   : Empties the feature cache associated with this
                  feature adaptor.
  Return type   : None
  Exceptions    : None
  Caller        : General
  Status        : At risk (under development)

Code:

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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

Code:

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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

Code:

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

Undocumented method

Code:

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public Listref Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_all ( )

  Example     : $operons = $operon_adaptor->fetch_all();
  Description : Similar to fetch_by_stable_id, but retrieves all
                operons stored in the database.
  Returntype  : listref of Bio::EnsEMBL::Operon
  Caller      : general
  Status      : At Risk

Code:

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

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

  Arg [1]    : listref of integers $id_list
               The unique database identifiers for the features to
               be obtained.
  Arg [2]    : optional - Bio::EnsEMBL::Slice to map features onto.
  Example    : @feats = @{$adaptor->fetch_all_by_dbID_list([1234, 2131, 982]))};
  Description: Returns the features created from the database
               defined by the the IDs in contained in the provided
               ID list $id_list.  The features will be returned
               in their native coordinate system.  That is, the
               coordinate system in which they are stored in the
               database.  In order to convert the features to a
               particular coordinate system use the transfer() or
               transform() method.  If none of the features are
               found in the database a reference to an empty list is
               returned.
  Returntype : listref of Bio::EnsEMBL::Features
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_logic_name ( ) [inherited]

  Arg [3]    : string $logic_name
               the logic name of the type of features to obtain
  Example    : $fs = $a->fetch_all_by_logic_name('foobar');
  Description: Returns a listref of features created from the database.
               only features with an analysis of type $logic_name will
               be returned.  If the logic name is invalid (not in the
               analysis table), a reference to an empty list will be
               returned.
  Returntype : listref of Bio::EnsEMBL::SeqFeatures
  Exceptions : thrown if no $logic_name
  Caller     : General
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig ( ) [inherited]

Description:

Deprecated:: use fetch_all_by_Slice instead

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_and_score ( ) [inherited]

Description:

Deprecated:: use fetch_all_by_Slice_and_score instead

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_constraint ( ) [inherited]

Description:

Deprecated:: use fetch_all_by_RawContig_constraint instead

Code:

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public Reference Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_all_by_Slice ( )

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice to fetch operons on.
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Arg [3]    : (optional) boolean $load_transcripts
               if true, transcripts will be loaded immediately rather than
               lazy loaded later.
  Arg [4]    : (optional) string $source
               the source name of the features to obtain.
  Arg [5]    : (optional) string biotype
                the biotype of the features to obtain.
  Example    : @operons = @{$operon_adaptor->fetch_all_by_Slice()};
  Description: Overrides superclass method to optionally load transcripts
               immediately rather than lazy-loading them later.  This
               is more efficient when there are a lot of operons whose
               transcripts are going to be used.
  Returntype : reference to list of operons 
  Exceptions : thrown if exon cannot be placed on transcript slice
  Caller     : Slice::get_all_operons
  Status     : Stable

Code:

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sub fetch_all_by_Slice {
    my ( $self, $slice, $logic_name, $load_transcripts ) = @_;

    my $constraint = '';
    my $operons =
      $self->SUPER::fetch_all_by_Slice_constraint( $slice, $constraint,
                                                   $logic_name );

    # If there are less than two operons, still do lazy-loading.
    if ( !$load_transcripts || @$operons < 2 ) {
        return $operons;
    }

    # Preload all of the transcripts now, instead of lazy loading later,
    # faster than one query per transcript.

    # First check if transcripts are already preloaded.
    # FIXME: Should check all transcripts.
    if ( exists( $operons->[0]->{'_operon_transcript_array'} ) ) {
        return $operons;
    }

    # Get extent of region spanned by transcripts.
    my ( $min_start, $max_end );
    foreach my $o (@$operons) {
        if ( !defined($min_start) || $o->seq_region_start() < $min_start ) {
            $min_start = $o->seq_region_start();
        }
        if ( !defined($max_end) || $o->seq_region_end() > $max_end ) {
            $max_end = $o->seq_region_end();
        }
    }

    my $ext_slice;

    if ( $min_start >= $slice->start() && $max_end <= $slice->end() ) {
        $ext_slice = $slice;
    } else {
        my $sa = $self->db()->get_SliceAdaptor();
        $ext_slice =
          $sa->fetch_by_region( $slice->coord_system->name(),
                                $slice->seq_region_name(),
                                $min_start,
                                $max_end,
                                $slice->strand(),
                                $slice->coord_system->version() );
    }

    # Associate transcript identifiers with operons.

    my %o_hash = map { $_->dbID => $_ } @{$operons};

    my $o_id_str = join( ',', keys(%o_hash) );

    my $sth =
      $self->prepare(   "SELECT operon_id, operon_transcript_id "
                      . "FROM   operon_transcript "
                      . "WHERE  operon_id IN ($o_id_str)" );

    $sth->execute();

    my ( $o_id, $tr_id );
    $sth->bind_columns( \( $o_id, $tr_id ) );

    my %tr_o_hash;

    while ( $sth->fetch() ) {
        $tr_o_hash{$tr_id} = $o_hash{$o_id};
    }

    my $ta = $self->db()->get_OperonTranscriptAdaptor();
    my $transcripts =
      $ta->fetch_all_by_Slice( $ext_slice,
                               1, undef,
                               sprintf( "ot.operon_transcript_id IN (%s)",
                                        join( ',',
                                              sort { $a <=> $b }
                                                keys(%tr_o_hash) ) ) );

    # Move transcripts onto operon slice, and add them to operons.
    foreach my $tr ( @{$transcripts} ) {
        if ( !exists( $tr_o_hash{ $tr->dbID() } ) ) { next }

        my $new_tr;
        if ( $slice != $ext_slice ) {
            $new_tr = $tr->transfer($slice);
            if ( !defined($new_tr) ) {
                throw(   "Unexpected. "
                       . "Transcript could not be transfered onto operon slice."
                );
            }
        } else {
            $new_tr = $tr;
        }

        $tr_o_hash{ $tr->dbID() }->add_OperonTranscript($new_tr);
    }

    return $operons;
} ## end sub fetch_all_by_Slice

Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_and_score ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) float $score
               lower bound of the the score of the features retrieved
  Arg [3]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Example    : $fts = $a->fetch_all_by_Slice_and_score($slice,90,'Swall');
  Description: Returns a list of features created from the database which are 
               are on the Slice defined by $slice and which have a score 
               greater than $score. If $logic_name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
  Exceptions : none
  Caller     : Bio::EnsEMBL::Slice
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_constraint ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [3]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Example    : $fs = $a->fetch_all_by_Slice_constraint($slc, 'perc_ident > 5');
  Description: Returns a listref of features created from the database which 
               are on the Slice defined by $slice and fulfill the SQL 
               constraint defined by $constraint. If logic name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
  Exceptions : thrown if $slice is not defined
  Caller     : Bio::EnsEMBL::Slice
  Status     : Stable

Code:

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sub fetch_all_by_Slice_constraint {
  my ( $self, $slice, $constraint, $logic_name ) = @_;


  my @result = ();

  if ( !ref($slice)
       || !(    $slice->isa('Bio::EnsEMBL::Slice')
             or $slice->isa('Bio::EnsEMBL::LRGSlice') ) )
  {
    throw("Bio::EnsEMBL::Slice argument expected.");
  }

  $constraint ||= '';
  $constraint =
    $self->_logic_name_to_constraint( $constraint, $logic_name );

  # If the logic name was invalid, undef was returned
  if ( !defined($constraint) ) { return [] }

  my $key;
  my $cache;

  # Will only use feature_cache if hasn't been no_cache attribute set
  if (
    !( defined( $self->db()->no_cache() ) && $self->db()->no_cache() ) )
  {

    #strain test and add to constraint if so to stop caching.
    if ( $slice->isa('Bio::EnsEMBL::StrainSlice') ) {
      my $string =
        $self->dbc()->db_handle()->quote( $slice->strain_name() );

      if ( $constraint ne "" ) {
        $constraint .= " AND $string = $string ";
      } else {
        $constraint .= " $string = $string ";
      }
    }

    # Check the cache and return the cached results if we have already
    # done this query.  The cache key is the made up from the slice
    # name, the constraint, and the bound parameters (if there are any).
    $key = uc( join( ':', $slice->name(), $constraint ) );

    my $bind_params = $self->bind_param_generic_fetch();

    if ( defined($bind_params) ) {
      $key .= ':'
        . join( ':', map { $_->[0] . '/' . $_->[1] } @{$bind_params} );
    }

    $cache = $self->_slice_feature_cache();
    if ( exists( $cache->{$key} ) ) {
      # Clear the bound parameters and return the cached data.
      $self->{'_bind_param_generic_fetch'} = ();
      return $cache->{$key};
    }
  } ## end if ( !( defined( $self...)))

  my $sa = $slice->adaptor();

  # Hap/PAR support: retrieve normalized 'non-symlinked' slices.
  my @proj = @{ $sa->fetch_normalized_slice_projection($slice) };


 
  if ( !@proj ) {
    throw( 'Could not retrieve normalized Slices. '
         . 'Database contains incorrect assembly_exception information.'
    );
  }

  # Want to get features on the FULL original slice as well as any
  # symlinked slices.

  # Filter out partial slices from projection that are on same
  # seq_region as original slice.

  my $sr_id = $slice->get_seq_region_id();

  @proj = grep { $_->to_Slice->get_seq_region_id() != $sr_id } @proj;

  my $segment = bless( [ 1, $slice->length(), $slice ],
                       'Bio::EnsEMBL::ProjectionSegment' );
  push( @proj, $segment );

  # construct list of Hap/PAR boundaries for entire seq region
  my @bounds;

  my $ent_slice = $sa->fetch_by_seq_region_id($sr_id);
  if ( $slice->strand() == -1 ) {
    $ent_slice = $ent_slice->invert();
  }

  my @ent_proj =
    @{ $sa->fetch_normalized_slice_projection($ent_slice) };
  shift(@ent_proj);    # skip first

  @bounds = map { $_->from_start() - $slice->start() + 1 } @ent_proj;


  # fetch features for the primary slice AND all symlinked slices
  foreach my $seg (@proj) {


    my $offset    = $seg->from_start();
    my $seg_slice = $seg->to_Slice();
    my $features =
      $self->_slice_fetch( $seg_slice, $constraint );

    # If this was a symlinked slice offset the feature coordinates as
    # needed.
    if ( $seg_slice->name() ne $slice->name() ) {

    FEATURE:
      foreach my $f ( @{$features} ) {
        if ( $offset != 1 ) {
          $f->{'start'} += $offset - 1;
          $f->{'end'}   += $offset - 1;
        }

        # discard boundary crossing features from symlinked regions
        foreach my $bound (@bounds) {
          if ( $f->{'start'} < $bound && $f->{'end'} >= $bound ) {
            next FEATURE;
          }
        }

        $f->{'slice'} = $slice;
        push( @result, $f );
      }
    } else {
      push( @result, @{$features} );
    }
  } ## end foreach my $seg (@proj)

  # Will only use feature_cache when set attribute no_cache in DBAdaptor
  if ( defined($key) ) {
    $cache->{$key} = \@result;
  }

  return \@result;
} ## end sub fetch_all_by_Slice_constraint

public Listref Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_all_versions_by_stable_id ( )

  Arg [1]     : String $stable_id 
                The stable ID of the operon to retrieve
  Example     : $operon = $operon_adaptor->fetch_all_versions_by_stable_id
                  ('ENSG00000148944');
  Description : Similar to fetch_by_stable_id, but retrieves all versions of a
                operon stored in the database.
  Returntype  : listref of Bio::EnsEMBL::Operon
  Exceptions  : if we cant get the operon in given coord system
  Caller      : general
  Status      : At Risk

Code:

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public Bio::EnsEMBL::Feature Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_by_dbID ( ) [inherited]

  Arg [1]    : int $id
               The unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234));
               $feat = $feat->transform('contig');
  Description: Returns the feature created from the database defined by the
               the id $id.  The feature will be returned in its native
               coordinate system.  That is, the coordinate system in which it
               is stored in the database.  In order to convert it to a
               particular coordinate system use the transfer() or transform()
               method.  If the feature is not found in the database then
               undef is returned instead
  Returntype : Bio::EnsEMBL::Feature or undef
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Operon Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_by_name ( )

  Arg [1]    : String $label - name of operon to fetch
  Example    : my $operon = $operonAdaptor->fetch_by_name("accBC");
  Description: Returns the operon which has the given display label or undef if
               there is none. If there are more than 1, only the first is
               reported.
  Returntype : Bio::EnsEMBL::Operon
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_by_operon_transcript ( )

Undocumented method

Code:

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public Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_by_operon_transcript_id ( )

Undocumented method

Code:

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public Bio::EnsEMBL::Operon Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_by_operon_transcript_stable_id ( )

  Arg [1]    : string $trans_stable_id
               transcript stable ID whose operon should be retrieved
  Example    : my $operon = $operon_adaptor->fetch_by_operon_transcript_stable_id
                 ('ENST0000234');
  Description: Retrieves a operon from the database via the stable ID of one of
               its transcripts
  Returntype : Bio::EnsEMBL::Operon
  Exceptions : none
  Caller     : operonral
  Status     : Stable

Code:

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public Bio::EnsEMBL::Operon Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_by_stable_id ( )

  Arg [1]    : String $id 
               The stable ID of the operon to retrieve
  Example    : $operon = $operon_adaptor->fetch_by_stable_id('ENSG00000148944');
  Description: Retrieves a operon object from the database via its stable id.
               The operon will be retrieved in its native coordinate system (i.e.
               in the coordinate system it is stored in the database). It may
               be converted to a different coordinate system through a call to
               transform() or transfer(). If the operon or exon is not found
               undef is returned instead.
  Returntype : Bio::EnsEMBL::Operon or undef
  Exceptions : if we cant get the operon in given coord system
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_Iterator_by_Slice ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : Optional string: logic name of analysis
  Arg [3]    : Optional int: Chunk size to iterate over. Default is 500000
  Example    : my $slice_iter = $feature_adaptor->fetch_Iterator_by_Slice($slice);

               while(my $feature = $slice_iter->next && defined $feature){
                 #Do something here
               }

  Description: Creates an Iterator which chunks the query Slice to facilitate
               large Slice queries which would have previously run out of memory
  Returntype : Bio::EnsEMBL::Utils::Iterator
  Exceptions : None
  Caller     : general
  Status     : at risk

Code:

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public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_Iterator_by_Slice_method ( ) [inherited]

  Arg [1]    : CODE ref of Slice fetch method
  Arg [2]    : ARRAY ref of parameters for Slice fetch method
  Arg [3]    : Optional int: Slice index in parameters array
  Arg [4]    : Optional int: Slice chunk size. Default=500000
  Example    : my $slice_iter = $feature_adaptor->fetch_Iterator_by_Slice_method
                               	      ($feature_adaptor->can('fetch_all_by_Slice_Arrays'),
	                                   \@fetch_method_params,
	                                   0,#Slice idx
	                                  );

               while(my $feature = $slice_iter->next && defined $feature){
                 #Do something here
               }

  Description: Creates an Iterator which chunks the query Slice to facilitate
               large Slice queries which would have previously run out of memory
  Returntype : Bio::EnsEMBL::Utils::Iterator
  Exceptions : Throws if mandatory params not valid
  Caller     : general
  Status     : at risk

Code:

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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

Code:

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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

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::get_seq_region_id_external ( ) [inherited]

Undocumented method

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::get_seq_region_id_internal ( ) [inherited]

Undocumented method

Code:

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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

Code:

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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

Code:

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public Listref Bio::EnsEMBL::DBSQL::OperonAdaptor::list_dbIDs ( )

  Example    : @operon_ids = @{$operon_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all operons in the current db
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : Listref of Ints
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::OperonAdaptor::list_seq_region_ids ( )

Undocumented method

Code:

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public Reference Bio::EnsEMBL::DBSQL::OperonAdaptor::list_stable_ids ( )

  Example    : @stable_operon_ids = @{$operon_adaptor->list_stable_ids()};
  Description: Gets an listref of stable ids for all operons in the current db
  Returntype : reference to a list of strings
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

  Arg [1]    : list of args @args
               Superclass constructor arguments
  Example    : none
  Description: Constructor which warns if caching has been switched off
  Returntype : Bio::EnsEMBL::BaseFeatureAdaptor
  Exceptions : none
  Caller     : implementing subclass constructors
  Status     : Stable

Code:

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

Reimplemented in Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, and Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor.

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

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

public void Bio::EnsEMBL::DBSQL::OperonAdaptor::remove ( )

  Arg [1]    : Bio::EnsEMBL::Operon $operon
               the operon to remove from the database
  Example    : $operon_adaptor->remove($operon);
  Description: Removes a operon completely from the database. All associated
               transcripts, exons, stable_identifiers, descriptions, etc.
               are removed as well. Use with caution!
  Returntype : none
  Exceptions : throw on incorrect arguments 
               warning if operon is not stored in this database
  Caller     : general
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.

public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_analysis_id ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_feature_id ( ) [inherited]

Undocumented method

Code:

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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_RawContig ( ) [inherited]

Description:

Deprecated:: use remove_by_Slice instead

Code:

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public void Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_Slice ( ) [inherited]

  Arg [1]    : Bio::Ensembl::Slice $slice
  Example    : $feature_adaptor->remove_by_Slice($slice);
  Description: This removes features from the database which lie on a region
               represented by the passed in slice.  Only features which are
               fully contained by the slice are deleted; features which overlap
               the edge of the slice are not removed.
               The table the features are removed from is defined by
               the abstract method_tablename.
  Returntype : none
  Exceptions : thrown if no slice is supplied
  Caller     : general
  Status     : Stable

Code:

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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

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public Boolean Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::start_equals_end ( ) [inherited]

  Arg [1]    : (optional) boolean $newval
  Example    : $bfa->start_equals_end(1);
  Description: Getter/Setter for the start_equals_end flag.  If set
               to true sub _slice_fetch will use a simplified sql to retrieve 1bp slices.
  Returntype : boolean
  Exceptions : none
  Caller     : EnsemblGenomes variation DB build
  Status     : Stable

Code:

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public The Bio::EnsEMBL::DBSQL::OperonAdaptor::store ( )

  Arg [1]    : Bio::EnsEMBL::Operon $operon
               The operon to store in the database
  Arg [2]    : ignore_release in xrefs [default 1] set to 0 to use release info 
               in external database references
  Example    : $operon_adaptor->store($operon);
  Description: Stores a operon in the database.
  Returntype : the database identifier (dbID) of the newly stored operon
  Exceptions : thrown if the $operon is not a Bio::EnsEMBL::Operon or if 
               $operon does not have an analysis object
  Caller     : general
  Status     : Stable

Code:

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sub store {
    my ( $self, $operon, $ignore_release ) = @_;

    if ( !ref $operon || !$operon->isa('Bio::EnsEMBL::Operon') ) {
        throw("Must store a operon object, not a $operon");
    }

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

    if ( $operon->is_stored($db) ) {
        return $operon->dbID();
    }
            my $analysis = $operon->analysis();
  throw("Operons must have an analysis object.") if(!defined($analysis));
    my $analysis_id;
    if ( $analysis->is_stored($db) ) {
        $analysis_id = $analysis->dbID();
    } else {
        $analysis_id = $db->get_AnalysisAdaptor->store( $analysis );
    }
    # ensure coords are correct before storing
    #$operon->recalculate_coordinates();

    my $seq_region_id;

    ( $operon, $seq_region_id ) = $self->_pre_store($operon);

    my $store_operon_sql = qq(
        INSERT INTO operon
           SET seq_region_id = ?,
               seq_region_start = ?,
               seq_region_end = ?,
               seq_region_strand = ?,
               display_label = ?,
               analysis_id = ?
  );
    
    if ( defined($operon->stable_id()) ) {
        my $created = $self->db->dbc->from_seconds_to_date($operon->created_date());
        my $modified = $self->db->dbc->from_seconds_to_date($operon->modified_date());
        $store_operon_sql .= ", stable_id = ?, version = ?, created_date = " . $created . ",modified_date = " . $modified;
    }

        # column status is used from schema version 34 onwards (before it was
    # confidence)

    my $sth = $self->prepare($store_operon_sql);
    $sth->bind_param( 1, $seq_region_id,           SQL_INTEGER );
    $sth->bind_param( 2, $operon->start(),         SQL_INTEGER );
    $sth->bind_param( 3, $operon->end(),           SQL_INTEGER );
    $sth->bind_param( 4, $operon->strand(),        SQL_TINYINT );
    $sth->bind_param( 5, $operon->display_label(), SQL_VARCHAR );
    $sth->bind_param( 6, $analysis_id,             SQL_INTEGER );

    if ( defined($operon->stable_id()) ) {
        $sth->bind_param( 7, $operon->stable_id(), SQL_VARCHAR );
        my $version = ($operon->version()) ? $operon->version() : 1;
        $sth->bind_param( 8, $version, SQL_INTEGER ); 
    }

    $sth->execute();
    $sth->finish();

    my $operon_dbID = $sth->{'mysql_insertid'};

    my $transcripts = $operon->get_all_OperonTranscripts();

    if ( $transcripts && scalar @$transcripts ) {
        my $transcript_adaptor = $db->get_OperonTranscriptAdaptor();
        for my $transcript (@$transcripts) {
            $transcript_adaptor->store( $transcript, $operon_dbID );
        }
    }

    # store the dbentries associated with this operon
    my $dbEntryAdaptor = $db->get_DBEntryAdaptor();

    foreach my $dbe ( @{ $operon->get_all_DBEntries } ) {
        $dbEntryAdaptor->store( $dbe, $operon_dbID, "Operon", $ignore_release );
    }

    # store operon attributes if there are any
    my $attrs = $operon->get_all_Attributes();
    if ( $attrs && scalar @$attrs ) {
        my $attr_adaptor = $db->get_AttributeAdaptor();
        $attr_adaptor->store_on_Operon( $operon, $attrs );
    }

    # set the adaptor and dbID on the original passed in operon not the
    # transfered copy
    $operon->adaptor($self);
    $operon->dbID($operon_dbID);

    return $operon_dbID;
} ## end sub store

Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.

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

Bio/EnsEMBL/DBSQL/OperonAdaptor.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation