Inheritance diagram for Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor:

Class Summary

Synopsis

  my $assembly_exception_feature_adaptor =
    $database_adaptor-\>get_AssemblyExceptionFeatureAdaptor();

  @assembly_exception_features =
    $assembly_exception_feature_adaptor-\>fetch_all_by_Slice($slice);

Description

Assembly Exception Feature Adaptor - database access for assembly
exception features.

Definition at line 25 of file AssemblyExceptionFeatureAdaptor.pm.

Available Methods
protected	_check_start_end_strand ()
protected	_columns ()
protected	_default_where_clause ()
protected	_final_clause ()
protected	_left_join ()
protected	_list_dbIDs ()
protected	_objs_from_sth ()
protected	_pre_store ()
protected	_remap ()
protected	_straight_join ()
protected	_tables ()
public Listref	bind_param_generic_fetch ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public	dump_data ()
public Reference	fetch_all ()
public Listref	fetch_all_by_dbID_list ()
public Reference	fetch_all_by_Slice ()
public Bio::EnsEMBL::AssemblyExceptionFeature	fetch_by_dbID ()
public Listref	generic_fetch ()
public	get_dumped_data ()
public Boolean	is_multispecies ()
public Scalar	last_insert_id ()
public Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor	new ()
public DBI::StatementHandle	prepare ()
public void	remove ()
public Int	species_id ()
public Int	store ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor::_check_start_end_strand ( )

Undocumented method

Code:

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

Undocumented method

Code:

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

Undocumented method

Code:

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

protected 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::BaseAdaptor::_objs_from_sth ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor::_pre_store ( )

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor::_remap ( )

Undocumented method

Code:

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sub _remap {
  my ($self, $features, $mapper, $slice) = @_;

  # check if any remapping is actually needed
  if(@$features && (!$features->[0]->isa('Bio::EnsEMBL::Feature') ||
                    $features->[0]->slice == $slice)) {
    return $features;
  }

  # remapping has not been done, we have to do our own conversion from
  # to slice coords

  my @out;

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

  my ($seq_region, $start, $end, $strand);

  my $slice_seq_region = $slice->seq_region_name();

  foreach my $f (@$features) {
    # since feats were obtained in contig coords, attached seq is a contig
    my $fslice = $f->slice();
    if(!$fslice) {
      throw("Feature does not have attached slice.\n");
    }
    my $fseq_region = $fslice->seq_region_name();
    my $fcs = $fslice->coord_system();

    if(!$slice_cs->equals($fcs)) {
      # slice of feature in different coord system, mapping required
      ($seq_region, $start, $end, $strand) =
        $mapper->fastmap($fseq_region,$f->start(),$f->end(),$f->strand(),$fcs);

      # undefined start means gap
      next if(!defined $start);
    } else {
      $start      = $f->start();
      $end        = $f->end();
      $strand     = $f->strand();
      $seq_region = $f->slice->seq_region_name();
    }

    # maps to region outside desired area
    next if ($start > $slice_end) || ($end < $slice_start) || 
      ($slice_seq_region ne $seq_region);

    # create new copies of successfully mapped feaatures with shifted start,
    # end and strand
    my ($new_start, $new_end);
    if($slice_strand == -1) {
      $new_start = $slice_end - $end + 1;
      $new_end = $slice_end - $start + 1;
    } else {
      $new_start = $start - $slice_start + 1;
      $new_end = $end - $slice_start + 1;
    }
    
    push @out, Bio::EnsEMBL::AssemblyExceptionFeature->new(
            '-dbID'            => $f->dbID,
            '-start'           => $new_start,
            '-end'             => $new_end,
            '-strand'          => $strand * $slice_strand,
            '-adaptor'         => $self,
            '-slice'           => $slice,
            '-alternate_slice' => $f->alternate_slice,
            '-type'            => $f->type,
    );
  }

  return \@out;
}

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

Undocumented method

Code:

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

Undocumented method

Code:

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

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

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 Reference Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor::fetch_all ( )

  Arg [1]    : none
  Example    : my @axfs = @{$axfa->fetch_all()};
  Description: Retrieves all assembly exception features which are in the
               database and builds internal caches of the features.
  Returntype : reference to list of Bio::EnsEMBL::AssemblyExceptionFeatures
  Exceptions : none
  Caller     : fetch_by_dbID, fetch_by_Slice
  Status     : Stable

Code:

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sub fetch_all {
  my $self = shift;

  # this is the "global" cache for all assembly exception features in the db
  if(defined($self->{'_aexc_cache'})) {
    return $self->{'_aexc_cache'};
  }

  my $statement = qq(
  SELECT    ae.assembly_exception_id,
            ae.seq_region_id,
            ae.seq_region_start,
            ae.seq_region_end,
            ae.exc_type,
            ae.exc_seq_region_id,
            ae.exc_seq_region_start,
            ae.exc_seq_region_end,
            ae.ori
  FROM      assembly_exception ae,
            coord_system cs,
            seq_region sr
  WHERE     cs.species_id = ?
    AND     sr.coord_system_id = cs.coord_system_id
    AND     sr.seq_region_id = ae.seq_region_id);

  my $sth = $self->prepare($statement);

  $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );

  $sth->execute();

  my ($ax_id, $sr_id, $sr_start, $sr_end,
      $x_type, $x_sr_id, $x_sr_start, $x_sr_end, $ori);

  $sth->bind_columns(\$ax_id, \$sr_id, \$sr_start, \$sr_end,
                     \$x_type, \$x_sr_id, \$x_sr_start, \$x_sr_end, \$ori);

  my @features;
  my $sa = $self->db()->get_SliceAdaptor();

  $self->{'_aexc_dbID_cache'} = {};

  while($sth->fetch()) {
    my $slice   = $sa->fetch_by_seq_region_id($sr_id);
    my $x_slice = $sa->fetch_by_seq_region_id($x_sr_id);

    # each row creates TWO features, each of which has alternate_slice
    # pointing to the "other" one

   
    my $a = Bio::EnsEMBL::AssemblyExceptionFeature->new
          ('-dbID'            => $ax_id,
           '-start'           => $sr_start,
           '-end'             => $sr_end,
           '-strand'          => 1,
           '-adaptor'         => $self,
           '-slice'           => $slice,
           '-alternate_slice' => $x_slice->sub_Slice($x_sr_start, $x_sr_end),
           '-type'            => $x_type);
   
    push @features, $a;
    $self->{'_aexc_dbID_cache'}->{$ax_id} = $a;

    push @features, Bio::EnsEMBL::AssemblyExceptionFeature->new
          ('-dbID'            => $ax_id,
           '-start'           => $x_sr_start,
           '-end'             => $x_sr_end,
           '-strand'          => 1,
           '-adaptor'         => $self,
           '-slice'           => $x_slice,
           '-alternate_slice' => $slice->sub_Slice($sr_start, $sr_end),
           '-type'            => "$x_type REF" );
  }

  $sth->finish();

  $self->{'_aexc_cache'} = \@features;
  
  return \@features;
}

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 Reference Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor::fetch_all_by_Slice ( )

  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Example    : my @axfs = @{$axfa->fetch_all_by_Slice($slice)};
  Description: Retrieves all assembly exception features which overlap the
               provided slice.  The returned features will be in coordinate
               system of the slice.
  Returntype : reference to list of Bio::EnsEMBL::AssemblyException features
  Exceptions : none
  Caller     : Feature::get_all_alt_locations, general
  Status     : Stable

Code:

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public Bio::EnsEMBL::AssemblyExceptionFeature Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor::fetch_by_dbID ( )

  Arg [1]    : int $dbID
  Example    : my $axf = $axfa->fetch_by_dbID(3);
  Description: Retrieves a single assembly exception feature via its internal
               identifier.  Note that this only retrieves one of the two
               assembly exception features which are represented by a single
               row in the assembly_exception table.
  Returntype : Bio::EnsEMBL::AssemblyExceptionFeature
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

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

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

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 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 Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor::new ( )

  Arg [1]    : list of args @args
               Superclass constructor arguments
  Example    : none
  Description: Constructor which just initializes internal cache structures
  Returntype : Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor
  Exceptions : none
  Caller     : implementing subclass constructors
  Status     : Stable

Code:

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

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::AssemblyExceptionFeatureAdaptor::remove ( )

  Arg [1]    : $asx Bio::EnsEMBL::AssemblyFeatureException 
  Example    : $asx_adaptor->remove($asx);
  Description: This removes a assembly exception feature from the database.  
  Returntype : none
  Exceptions : thrown if $asx arg does not implement dbID(), or if
               $asx->dbID is not a true value
  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 Int Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor::store ( )

    Arg[1]       : Bio::EnsEMBL::AssemblyException $asx
    Arg[2]       : Bio::EnsEMBL::AssemblyException $asx2

    Example      : $asx = Bio::EnsEMBL::AssemblyExceptionFeature->new(...)
                   $asx2 = Bio::EnsEMBL::AssemblyExceptionFeature->new(...)
                   $asx_seq_region_id = $asx_adaptor->store($asx);
    Description:  This stores a assembly exception feature in the 
                  assembly_exception table and returns the assembly_exception_id.
                  Needs 2 features: one pointing to the Assembly_exception, and the
                  other pointing to the region in the reference that is being mapped to
                  Will check that start, end and type are defined, and the alternate
                  slice is present as well.
    ReturnType:   int
    Exceptions:   throw if assembly exception not defined (needs start, end,
		  type and alternate_slice) of if $asx not a Bio::EnsEMBL::AssemblyException
    Caller:       general
    Status:       Stable

Code:

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sub store{
  my $self = shift;
  my $asx = shift;
  my $asx2 = shift;


  if (! $asx->isa('Bio::EnsEMBL::AssemblyExceptionFeature')){
    throw("$asx is not a Ensembl assemlby exception -- not stored");
  }
  #if already present, return ID in the database
  my $db = $self->db();
  if ($asx->is_stored($db)){
    return $asx->dbID();
  }
  #do some checkings for the object
  #at the moment, the orientation is always 1
  if (! $asx->start || ! $asx->end ){
    throw("Assembly exception does not have coordinates");
  }
  if ($asx->type !~ /PAR|HAP|PATCH_NOVEL|PATCH_FIX/){
    throw("Only types of assembly exception features valid are PAR, HAP, PATCH_FIX or PATCH_NOVEL");
  }
  if ( !($asx->alternate_slice->isa('Bio::EnsEMBL::Slice')) ){
    throw("Alternate slice should be a Bio::EnsEMBL::Slice");
  }
  #now check the other Assembly exception feature, the one pointing to the REF
  # region
  if (!$asx2->isa('Bio::EnsEMBL::AssemblyExceptionFeature')){
    throw("$asx2 is not a Ensembl assemlby exception -- not stored");
  }
  if (! $asx2->start || ! $asx2->end ){
    throw("Assembly exception does not have coordinates");
  }
  if ($asx2->type !~ /HAP REF|PAR REF|PATCH_NOVEL REF|PATCH_FIX REF/){
    throw("$asx2 should have  type of assembly exception features HAP REF, PAR REF, PATCH_FIX REF or PATCH_NOVEL REF");
  }
  if (! ($asx2->alternate_slice->isa('Bio::EnsEMBL::Slice')) ){
    throw("Alternate slice should be a Bio::EnsEMBL::Slice");
  }
  #finally check that both features are pointing to each other slice
  if ($asx->slice != $asx2->alternate_slice || $asx->alternate_slice != $asx2->slice){
    throw("Slice and alternate slice in both features are not pointing to each other");
  }
  #prepare the SQL
  my $asx_sql = q{
    INSERT INTO assembly_exception( seq_region_id, seq_region_start,
                    seq_region_end, 
                    exc_type, exc_seq_region_id,
                    exc_seq_region_start, exc_seq_region_end,
                    ori)
        VALUES (?, ?, ?, ?, ?, ?, ?, 1)
    };
  
  my $asx_st = $self->prepare($asx_sql);
  my $asx_id = undef;
  my $asx_seq_region_id;
  my $asx2_seq_region_id;
  my $original = $asx;
  my $original2 = $asx2;
  #check all feature information
  ($asx, $asx_seq_region_id) = $self->_pre_store($asx);
  ($asx2, $asx2_seq_region_id) = $self->_pre_store($asx2);
  
  #and store it
  $asx_st->bind_param(1, $asx_seq_region_id, SQL_INTEGER);
  $asx_st->bind_param(2, $asx->start(), SQL_INTEGER);
  $asx_st->bind_param(3, $asx->end(), SQL_INTEGER);
  $asx_st->bind_param(4, $asx->type(), SQL_VARCHAR);
  $asx_st->bind_param(5, $asx2_seq_region_id, SQL_INTEGER);
  $asx_st->bind_param(6, $asx2->start(), SQL_INTEGER);
  $asx_st->bind_param(7, $asx2->end(), SQL_INTEGER);
  
  $asx_st->execute();
  $asx_id = $asx_st->{'mysql_insertid'};
  
  #finally, update the dbID and adaptor of the asx and asx2
  $original->adaptor($self);
  $original->dbID($asx_id);
  $original2->adaptor($self);
  $original2->dbID($asx_id);
  #and finally update dbID cache with new assembly exception
  $self->{'_aexc_dbID_cache'}->{$asx_id} = $original;
  #and update the other caches as well
  push @{$self->{'_aexc_slice_cache'}->{uc($asx->slice->name)}},$original, $original2;
  push @{$self->{'_aexc_cache'}}, $original, $original2;
  
  return $asx_id;
}

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

Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation