Inheritance diagram for Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor:

Class Summary

Synopsis

  $pafa =
    $registry-\>get_adaptor( 'Human', 'Core', 'ProteinAlignFeature' );

  my @features = @{ $pafa-\>fetch_all_by_Slice($slice) };

  $pafa-\>store(@features);

Definition at line 18 of file ProteinAlignFeatureAdaptor.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 Listref	_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	fetch_all ()
public Listref	fetch_all_by_dbID_list ()
public Listref	fetch_all_by_hit_name ()
public Listref	fetch_all_by_hit_name_unversioned ()
public Listref	fetch_all_by_logic_name ()
public	fetch_all_by_RawContig ()
public	fetch_all_by_RawContig_and_pid ()
public	fetch_all_by_RawContig_and_score ()
public	fetch_all_by_RawContig_constraint ()
public Listref	fetch_all_by_Slice ()
public Listref	fetch_all_by_Slice_and_external_db ()
public Listref	fetch_all_by_Slice_and_hcoverage ()
public Listref	fetch_all_by_Slice_and_pid ()
public Listref	fetch_all_by_Slice_and_score ()
public Listref	fetch_all_by_Slice_constraint ()
public Bio::EnsEMBL::Feature	fetch_by_dbID ()
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 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 void	store ()

Method Documentation

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

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor::_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::ProteinAlignFeatureAdaptor::_left_join ( )

Undocumented method

Code:

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

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

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protected Listref Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor::_objs_from_sth ( )

  Arg [1]    : DBI statement handle $sth
               an exectuted DBI statement handle generated by selecting 
               the columns specified by _columns() from the table specified 
               by _table()
  Example    : @dna_dna_align_feats = $self->_obj_from_hashref
  Description: PROTECTED implementation of superclass abstract method. 
               Creates DnaDnaAlignFeature objects from a DBI hashref
  Returntype : listref of Bio::EnsEMBL::ProteinAlignFeatures
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
  Status     : Stable

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 @features;
  my %analysis_hash;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;

  my ($protein_align_feature_id, $seq_region_id, $seq_region_start,
      $seq_region_end, $analysis_id, $seq_region_strand, $hit_start,
      $hit_end, $hit_name, $cigar_line, $evalue, $perc_ident, $score,
      $external_db_id, $hcoverage, $external_db_name, $external_display_db_name );

  $sth->bind_columns(\$protein_align_feature_id, \$seq_region_id,
           \$seq_region_start,\$seq_region_end, \$analysis_id,
           \$seq_region_strand, \$hit_start,\$hit_end, \$hit_name,
           \$cigar_line, \$evalue, \$perc_ident, \$score,
           \$external_db_id, \$hcoverage, \$external_db_name, \$external_display_db_name );

  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 $dest_slice_sr_id;
  if($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_sr_id  = $dest_slice->get_seq_region_id();
  }

  FEATURE: while($sth->fetch()) {
    #get the analysis object
    my $analysis = $analysis_hash{$analysis_id} ||=
      $aa->fetch_by_dbID($analysis_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 FEATURE 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} ||=
#          $sa->fetch_by_seq_region_id($asm_cs_name, $sr_name, undef, undef, undef,
#                               $asm_cs_vers);
#      }
    }

    #
    # 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_sr_id ne $seq_region_id )) {
    next FEATURE;
      }
      $slice = $dest_slice;
    }

    # Finally, create the new ProteinAlignFeature.
    push(
      @features,
      $self->_create_feature_fast(
        'Bio::EnsEMBL::DnaPepAlignFeature', {
          'slice'        => $slice,
          'start'        => $seq_region_start,
          'end'          => $seq_region_end,
          'strand'       => $seq_region_strand,
          'hseqname'     => $hit_name,
          'hstart'       => $hit_start,
          'hend'         => $hit_end,
          'hstrand'      => 1,                  # dna_pep_align features
                                                # are always hstrand 1
          'score'        => $score,
          'p_value'      => $evalue,
          'percent_id'   => $perc_ident,
          'cigar_string' => $cigar_line,
          'analysis'     => $analysis,
          'adaptor'      => $self,
          'dbID'           => $protein_align_feature_id,
          'external_db_id' => $external_db_id,
          'hcoverage'      => $hcoverage,
      'dbname'         => $external_db_name,
      'db_display_name' => $external_display_db_name
        } ) );

  }

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

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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::ProteinAlignFeatureAdaptor::_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

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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)

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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::BaseAdaptor::fetch_all ( ) [inherited]

Undocumented method

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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::BaseAlignFeatureAdaptor::fetch_all_by_hit_name ( ) [inherited]

  Arg [1]    : string $hit_name
               The hit_name of the features to obtain
  Arg [2]    : (optional) string $logic_name
               The analysis logic name of the type of features to
               obtain.
  Example    : @feats =
                 @{ $adaptor->fetch_all_by_hit_name( $name,
                   $logic_name ); }
  Description: Returns a listref of features created from the
               database which correspond to the given hit_name.  If
               logic name is defined, only features with an analysis
               of type $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
  Exceptions : thrown if hit_name is not defined
  Caller     : general
  Status     : Stable

Code:

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public Listref Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_hit_name_unversioned ( ) [inherited]

  Arg [1]    : string $hit_name
               The beginning of the hit_name of the features to
               obtain, e.g. AA768786 would retrieve AA768786.1,
               AA768786.2 etc.
  Arg [2]    : (optional) string $logic_name
               The analysis logic name of the type of features to
               obtain.
  Example    : @feats =
                  @{ $adaptor->fetch_all_by_hit_name( $name,
                    $logic_name ) };
  Description: Returns a listref of features created from the
               database which start with the given hit_name.  If
               logic name is defined, only features with an analysis
               of type $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
  Exceptions : thrown if hit_name is not defined
  Caller     : general
  Status     : At risk

Code:

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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::BaseAlignFeatureAdaptor::fetch_all_by_RawContig_and_pid ( ) [inherited]

Description:

Deprecated:: use fetch_all_by_Slice_and_pid 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 Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Example    : $fts = $a->fetch_all_by_Slice($slice, 'Swall');
  Description: Returns a listref of features created from the database 
               which are on the Slice defined by $slice. If $logic_name is 
               defined only features with an analysis of type $logic_name 
               will be returned. 
               NOTE: only features that are entirely on the slice's seq_region
               will be returned (i.e. if they hang off the start/end of a
               seq_region they will be discarded). Features can extend over the
               slice boundaries though (in cases where you have a slice that
               doesn't span the whole seq_region).
  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::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventAdaptor, and Bio::EnsEMBL::DBSQL::TranscriptAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_Slice_and_external_db ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice from which to obtain align features.
  Arg [2]    : String $external_db_name
               Name of the external DB to which the align features
               should be restricted.
  Arg [3]    : (optional) string $logic_name
               The logic name of the type of features to obtain.
  Example    : @feats = @{
                  $adaptor->fetch_all_by_Slice_and_external_db( $slice,
                    'EMBL' ) };
  Description: Returns a listref of features created from the
               database which are on the Slice $slice and associated
               with external DB $external_db_name.  If logic name
               is defined, only features with an analysis of type
               $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
               in Slice coordinates
  Exceptions : thrown if $external_db_name is not defined or if
               the subclass does not return a table alias for the
               external_db table from _tables()
  Caller     : general
  Status     : At Risk

Code:

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public Listref Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_Slice_and_hcoverage ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice from which to obtain align features.
  Arg [2]    : (optional) float $hcoverage 
               A lower bound for the hcoverage of feats to obtain.
  Arg [3]    : (optional) string $logic_name
               The logic name of the type of features to obtain.
  Example    : @feats = @{
                $adaptor->fetch_all_by_Slice_and_hcoverage( $slice,
                  50.0 ) };
  Description: Returns a listref of features created from the
               database which are on the Slice $slice and with a
               hcoverage greater than $hcoverage.  If logic name
               is defined, only features with an analysis of type
               $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
               in Slice coordinates
  Exceptions : none
  Caller     : general
  Status     : At Risk

Code:

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public Listref Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_Slice_and_pid ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice from which to obtain align features.
  Arg [2]    : (optional) float $pid 
               A lower bound for the percentage identity of features
               to obtain.
  Arg [3]    : (optional) string $logic_name
               The logic name of the type of features to obtain.
  Example    : @feats =
                 @{ $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 ) };
  Description: Returns a listref of features created from the
               database which are on the Slice $slice and with a
               percentage identity greater than $pid.  If logic name
               is defined, only features with an analysis of type
               $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
               in Slice coordinates
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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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 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::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::ProteinAlignFeatureAdaptor::list_dbIDs ( )

  Arg [1]    : none
  Example    : @feature_ids = @{$protein_align_feature_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all protein align 
               features 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     : ?
  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

Code:

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

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

  Arg [1]    : A feature $feature 
  Example    : $feature_adaptor->remove($feature);
  Description: This removes a feature from the database.  The table the
               feature is removed from is defined by the abstract method
               _tablename, and the primary key of the table is assumed
               to be _tablename() . '_id'.  The feature argument must 
               be an object implementing the dbID method, and for the
               feature to be removed from the database a dbID value must
               be returned.
  Returntype : none
  Exceptions : thrown if $feature arg does not implement dbID(), or if
               $feature->dbID is not a true value
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::PredictionExonAdaptor, Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor, and Bio::EnsEMBL::DBSQL::TranscriptAdaptor.

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

Undocumented method

Code:

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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

Code:

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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 void Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor::store ( )

  Arg [1]    : list of Bio::EnsEMBL::DnaPepAlignFeature @feats
  Example    : $protein_align_feature_adaptor->store(@feats);
  Description: stores a list of ProteinAlignFeatures in the database
  Returntype : none
  Exceptions : throw if any of the provided features cannot be stored
               which may occur if:
 The feature does not have an associated Slice
 The feature does not have an associated analysis
 The Slice the feature is associated with is on a seq_region
                   unknown to this database
              A warning is given if:
 The feature has already been stored in this db
  Caller     : Pipeline
  Status     : Stable

Code:

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

  throw("Must call store with features") if( scalar(@feats) == 0 );

  my @tabs = $self->_tables;
  my ($tablename) = @{$tabs[0]};

  my $db = $self->db();
  my $slice_adaptor = $db->get_SliceAdaptor();
  my $analysis_adaptor = $db->get_AnalysisAdaptor();

  my $sth = $self->prepare(
     "INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end,
                             seq_region_strand, hit_start, hit_end,
                             hit_name, cigar_line,
                             analysis_id, score, evalue, perc_ident, external_db_id, hcoverage)
     VALUES (?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?)");

 FEATURE: foreach my $feat ( @feats ) {
   if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaPepAlignFeature") ) {
     throw("feature must be a Bio::EnsEMBL::DnaPepAlignFeature,"
           . " not a [".ref($feat)."].");
   }

   if($feat->is_stored($db)) {
     warning("PepDnaAlignFeature [".$feat->dbID."] is already stored" .
             " in this database.");
     next FEATURE;
   }

   #sanity check the hstart and hend
   my $hstart  = $feat->hstart();
   my $hend    = $feat->hend();
   $self->_check_start_end_strand($hstart,$hend,1);

   my $cigar_string = $feat->cigar_string();
   if(!$cigar_string) {
     $cigar_string = $feat->length() . 'M';
     warning("DnaPepAlignFeature does not define a cigar_string.\n" .
             "Assuming ungapped block with cigar_string=$cigar_string\n");
   }

   my $hseqname = $feat->hseqname();
   if(!$hseqname) {
     throw("DnaPepAlignFeature must define an hseqname.");
   }

   if(!defined($feat->analysis)) {
     throw("An analysis must be attached to the features to be stored.");
   }

   #store the analysis if it has not been stored yet
   if(!$feat->analysis->is_stored($db)) {
     $analysis_adaptor->store($feat->analysis());
   }

   my $slice = $feat->slice();
   if(!defined($slice) || !($slice->isa("Bio::EnsEMBL::Slice") or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
     throw("A slice must be attached to the features to be stored.");
   }

   my $original = $feat;
   my $seq_region_id;
   ($feat, $seq_region_id) = $self->_pre_store($feat);

   $sth->bind_param(1,$seq_region_id,SQL_INTEGER);
   $sth->bind_param(2,$feat->start,SQL_INTEGER);
   $sth->bind_param(3,$feat->end,SQL_INTEGER);
   $sth->bind_param(4,$feat->strand,SQL_TINYINT);
   $sth->bind_param(5,$feat->hstart,SQL_INTEGER);
   $sth->bind_param(6,$feat->hend,SQL_INTEGER);
   $sth->bind_param(7,$feat->hseqname,SQL_VARCHAR);
   $sth->bind_param(8,$feat->cigar_string,SQL_LONGVARCHAR);
   $sth->bind_param(9,$feat->analysis->dbID,SQL_INTEGER);
   $sth->bind_param(10,$feat->score,SQL_DOUBLE);
   $sth->bind_param(11,$feat->p_value,SQL_DOUBLE);
   $sth->bind_param(12,$feat->percent_id,SQL_REAL);
   $sth->bind_param(13,$feat->external_db_id,SQL_INTEGER);
   $sth->bind_param(14,$feat->hcoverage,SQL_DOUBLE);

   $sth->execute();
   $original->dbID($sth->{'mysql_insertid'});
   $original->adaptor($self);
 }

 $sth->finish();
}

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

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

Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm

Class Summary

Synopsis

Available Methods

Method Documentation