Inheritance diagram for Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor:

Class Summary

Synopsis

  use Bio::EnsEMBL::Registry;

  Bio::EnsEMBL::Registry-\>load_registry_from_db(
    -host =\> 'ensembldb.ensembl.org',
    -user =\> 'anonymous'
  );

  $pfa = Bio::EnsEMBL::Registry-\>get_adaptor( "human", "core",
    "proteinfeature" );

  my @prot_feats = @{ $pfa-\>fetch_all_by_translation_id(1231) };

  my $prot_feat = $pfa-\>fetch_by_dbID(523);

Definition at line 25 of file ProteinFeatureAdaptor.pm.

Available Methods
protected	_columns ()
protected	_default_where_clause ()
protected	_final_clause ()
protected	_left_join ()
protected	_list_dbIDs ()
protected	_objs_from_sth ()
protected	_straight_join ()
protected	_tables ()
public Listref	bind_param_generic_fetch ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public	dump_data ()
public	fetch_all ()
public Listref	fetch_all_by_dbID_list ()
public	fetch_all_by_feature_and_dbID ()
public Listref	fetch_all_by_translation_id ()
public Bio::EnsEMBL::ProteinFeauture	fetch_by_dbID ()
public	fetch_by_translation_id ()
public Listref	generic_fetch ()
public	get_dumped_data ()
public Boolean	is_multispecies ()
public Scalar	last_insert_id ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()
public DBI::StatementHandle	prepare ()
public	save ()
public Int	species_id ()
public Int	store ()

Method Documentation

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

Undocumented method

Code:

click to view

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

Undocumented method

Code:

click to view

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:

click to view

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:

click to view

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:

click to view

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

Undocumented method

Code:

click to view

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

Undocumented method

Code:

click to view

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

Undocumented method

Code:

click to view

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:

click to view

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:

click to view

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:

click to view

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

Undocumented method

Code:

click to view

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

Undocumented method

Code:

click to view

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:

click to view

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

public Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::fetch_all_by_feature_and_dbID ( )

Undocumented method

Code:

click to view

public Listref Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::fetch_all_by_translation_id ( )

  Arg [1]    : int $transl
               the internal id of the translation corresponding to protein 
               whose features are desired 
  Example    : @prot_feats =
                  @{ $prot_feat_adaptor->fetch_by_translation_id(1234) };
  Description: Gets all protein features present on a peptide using the
               translations internal identifier.  This method will return
               an unsorted list of all protein_feature types.  The feature
               types may be distinguished using the logic name attribute of
               the attached analysis objects.   
  Returntype : listref of Bio::EnsEMBL::ProteinFeatures
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

click to view

public Bio::EnsEMBL::ProteinFeauture Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::fetch_by_dbID ( )

  Arg [1]    : int $protfeat_id
               the unique database identifier of the protein feature to obtain
  Example    : my $feature = $prot_feat_adaptor->fetch_by_dbID();
  Description: Obtains a protein feature object via its unique id
  Returntype : Bio::EnsEMBL::ProteinFeauture
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

click to view

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

public Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::fetch_by_translation_id ( )

Undocumented method

Code:

click to view

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:

click to view

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:

click to view

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:

click to view

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:

click to view

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

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

Code:

click to view

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:

click to view

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

public Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::save ( )

Undocumented method

Code:

click to view

sub save {
    
  my ($self, $features) = @_;

  my @feats = @$features;
  throw("Must call save with features") if( scalar(@feats) == 0 );

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

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

  my $sql = qq{INSERT INTO $tablename (translation_id, seq_start, seq_end, hit_start, hit_end, hit_name, analysis_id, score, evalue, perc_ident, external_data) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)};

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

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

     my $hstart = defined $feat->hstart ? $feat->hstart : $feat->start ;
     my $hend   = defined $feat->hend ? $feat->hend : $feat->end;

     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 $original = $feat;
     my $extra_data = $feat->extra_data ? $self->dump_data($feat->extra_data) : '';

     $sth->bind_param(1,$feat->translation_id,SQL_INTEGER);
     $sth->bind_param(2,$feat->start,SQL_INTEGER);
     $sth->bind_param(3,$feat->end,SQL_INTEGER);
     $sth->bind_param(4,$hstart,SQL_INTEGER);
     $sth->bind_param(5,$hend,SQL_INTEGER);
     $sth->bind_param(6,$feat->hseqname,SQL_VARCHAR);
     $sth->bind_param(7,$feat->analysis->dbID,SQL_INTEGER);
     $sth->bind_param(8,$feat->score,SQL_DOUBLE);
     $sth->bind_param(9,$feat->p_value,SQL_DOUBLE);
     $sth->bind_param(10,$feat->percent_id,SQL_FLOAT);
     $sth->bind_param(11,$extra_data,SQL_LONGVARCHAR);
     
     $sth->execute();
     $original->dbID($sth->{'mysql_insertid'});
     $original->adaptor($self);
 }

  $sth->finish();
}

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:

click to view

public Int Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::store ( )

  Arg [1]    : Bio::EnsEMBL::ProteinFeature $feature
               The feature to be stored
  Arg [2]    : int $translation_id

  Example    : $protein_feature_adaptor->store($protein_feature);
  Description: Stores a protein feature in the database
  Returntype : int - the new internal identifier of the stored protein feature
  Exceptions : thrown if arg is not a Bio::EnsEMBL:
  Caller     : none
  Status     : Stable

Code:

click to view

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

  if(!ref($feature) || !$feature->isa('Bio::EnsEMBL::ProteinFeature')) {
    throw("ProteinFeature argument is required");
  }

  if(!$translation_id) {
    deprecate("Calling ProteinFeatureAdaptor without a translation_id is " .
              "deprecated.  Pass a translation_id argument rather than " .
              "setting the ProteinFeature seqname to be the translation " .
              "id");
    $translation_id = $feature->seqname();
  }

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

  if($feature->is_stored($db)) {
    warning("ProteinFeature " . $feature->dbID() . " is already stored in " .
            "this database - not storing again");
  }

  my $analysis = $feature->analysis();
  if (!defined($analysis)) {
    throw("Feature doesn't have analysis. Can't write to database");
  }

  if(!$analysis->is_stored($db)) {
    $db->get_AnalysisAdaptor->store($analysis);
  }

  my $sth = 
    $self->prepare("INSERT INTO protein_feature " .
                   "        SET translation_id = ?, " .
                   "            seq_start      = ?, ".
                   "            seq_end        = ?, ".
                   "            analysis_id    = ?, ".
                   "            hit_start      = ?, ".
                   "            hit_end        = ?, ".
                   "            hit_name       = ?, ".
                   "            score          = ?, ".
                   "            perc_ident     = ?, ".
                   "            evalue         = ?");

  $sth->bind_param(1,$translation_id,SQL_INTEGER);
  $sth->bind_param(2,$feature->start,SQL_INTEGER);
  $sth->bind_param(3,$feature->end,SQL_INTEGER);
  $sth->bind_param(4,$analysis->dbID,SQL_INTEGER);
  $sth->bind_param(5,$feature->hstart,SQL_INTEGER);
  $sth->bind_param(6,$feature->hend,SQL_INTEGER);
  $sth->bind_param(7,$feature->hseqname,SQL_VARCHAR);
  $sth->bind_param(8,$feature->score,SQL_DOUBLE);
  $sth->bind_param(9,$feature->percent_id,SQL_FLOAT);
  $sth->bind_param(10,$feature->p_value,SQL_DOUBLE);

  $sth->execute();
  
  my $dbID = $sth->{'mysql_insertid'};

  $feature->adaptor($self);
  $feature->dbID($dbID);
  
  $sth->finish();

  return $dbID;          
}

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

Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm

Class Summary

Synopsis

Available Methods

Method Documentation