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

Public Member Functions
public Listref	fetch_all_by_translation_id ()

public Listref	fetch_all_by_logic_name ()

public Bio::EnsEMBL::ProteinFeauture	fetch_by_dbID ()

public Int	store ()

protected	_tables ()

protected	_left_join ()

protected	_tbl_columns ()

protected	_columns ()

protected	_objs_from_sth ()

public Listref	fetch_all_by_uniprot_acc ()

public	fetch_all_by_Slice_and_hcoverage ()

public	fetch_all_by_Slice_and_external_db ()

public	fetch_all_by_Slice_and_pid ()

public	fetch_all_by_Slice ()

public	fetch_Iterator_by_Slice_method ()

public	fetch_Iterator_by_Slice ()

public	fetch_all_by_Slice_and_score ()

public	fetch_all_by_Slice_constraint ()

public	fetch_all_by_stable_id_list ()

public	count_by_Slice_constraint ()

public	remove_by_Slice ()

public	get_seq_region_id_internal ()

public	get_seq_region_id_external ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor
public Listref	fetch_all_by_Slice_and_hcoverage ()

public Listref	fetch_all_by_Slice_and_external_db ()

public Listref	fetch_all_by_Slice_and_pid ()

public Listref	fetch_all_by_hit_name ()

public Listref	fetch_all_by_hit_name_unversioned ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
public Bio::EnsEMBL::BaseFeatureAdaptor	new ()

public Boolean	start_equals_end ()

public void	clear_cache ()

protected	_clear_slice_feature_cache ()

protected Bio::EnsEMBL::Utils::Cache	_slice_feature_cache ()

public Listref	fetch_all_by_Slice ()

public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice_method ()

public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice ()

public Listref	fetch_all_by_Slice_and_score ()

public Listref	fetch_all_by_Slice_constraint ()

public Listref	fetch_all_by_logic_name ()

public Listref	fetch_all_by_stable_id_list ()

protected	_create_feature ()

protected	_create_feature_fast ()

public Int	count_by_Slice_constraint ()

protected ArrayRef	_get_and_filter_Slice_projections ()

protected ArrayRef	_generate_feature_bounds ()

protected Listref	_get_by_Slice ()

protected	_slice_fetch ()

public	get_seq_region_id_external ()

public	get_seq_region_id_internal ()

protected	_pre_store ()

protected	_pre_store_userdata ()

protected	_check_start_end_strand ()

protected	_remap ()

protected	_seq_region_boundary_from_db ()

public void	store ()

public void	remove ()

public void	remove_by_Slice ()

protected	_max_feature_length ()

protected	_list_seq_region_ids ()

public	remove_by_analysis_id ()

public	remove_by_feature_id ()

public Bio::EnsEMBL::Feature	fetch_nearest_by_Feature ()

public Listref	fetch_all_by_outward_search ()

public Listref	fetch_all_nearest_by_Feature ()

public Listref	select_nearest ()

protected Int	_compute_nearest_end ()

protected Int	_compute_prime_distance ()

protected Int	_compute_midpoint ()

protected	_discard_excess_features_from_matrix ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()

public DBI::StatementHandle	prepare ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()

public Boolean	is_multispecies ()

public Int	species_id ()

protected	_list_dbIDs ()

protected	_straight_join ()

protected	_can_straight_join ()

public Listref	bind_param_generic_fetch ()

protected	_bind_param_generic_fetch ()

public String	generate_in_constraint ()

public Listref	generic_fetch ()

public Int	generic_count ()

protected	_generate_sql ()

public Bio::EnsEMBL::Feature	fetch_by_dbID ()

protected	_uncached_fetch_by_dbID ()

public Listref	fetch_all_by_dbID_list ()

protected	_uncached_fetch_all_by_dbID_list ()

protected ArrayRef	_uncached_fetch_all_by_id_list ()

public	fetch_all ()

public Scalar	last_insert_id ()

public	insert_ignore_clause ()

protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()

protected Boolean	_no_id_cache ()

public Boolean	ignore_cache_override ()

public Int	schema_version ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

protected	_build_id_cache ()

protected	_logic_name_to_constraint ()

Detailed Description

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 26 of file ProteinFeatureAdaptor.pm.

Member Function Documentation

◆ _columns()

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

Undocumented method

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◆ _left_join()

protected Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::_left_join ( )

Undocumented method

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◆ _objs_from_sth()

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

Undocumented method

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◆ _tables()

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

Undocumented method

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◆ _tbl_columns()

protected Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::_tbl_columns ( )

Undocumented method

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◆ count_by_Slice_constraint()

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

Undocumented method

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◆ fetch_all_by_logic_name()

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

  Arg [1]    : 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::ProteinFeatures
  Exceptions : thrown if no $logic_name
  Caller     : General
  Status     : Stable

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◆ fetch_all_by_Slice()

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

Undocumented method

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◆ fetch_all_by_Slice_and_external_db()

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

Undocumented method

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◆ fetch_all_by_Slice_and_hcoverage()

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

Undocumented method

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◆ fetch_all_by_Slice_and_pid()

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

Undocumented method

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◆ fetch_all_by_Slice_and_score()

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

Undocumented method

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◆ fetch_all_by_Slice_constraint()

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

Undocumented method

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◆ fetch_all_by_stable_id_list()

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

Undocumented method

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◆ fetch_all_by_translation_id()

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

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◆ fetch_all_by_uniprot_acc()

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

  Arg [1]    : string uniprot accession
               The uniprot accession of the features to obtain
  Arg [2]    : (optional) string $logic_name
               The analysis logic name of the type of features to
               obtain. Default is 'gifts_import'
  Example    :

@feats =
                @{ $adaptor->fetch_all_by_uniprot_acc( 'P20366',
                  'gifts_import' ); }

  Description: Returns a listref of features created from the
               database which correspond to the given uniprot accession.  If
               logic name is defined, only features with an analysis
               of type $logic_name will be returned. Defaults to 'gifts_import'
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
  Exceptions : thrown if uniprot_acc is not defined
  Caller     : general
  Status     : Stable

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◆ fetch_by_dbID()

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

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sub fetch_by_dbID {
  my ($self, $protfeat_id) = @_;
 
  my @select_cols = $self->_tbl_columns(1); # skip pk - protein_feature_id
  my @select_cols_alias = map { 'pf.'.$_ } @select_cols;
  my $select_sql = "SELECT ". (join ',', @select_cols_alias);
 
  $select_sql .=              ", x.description, x.display_label, i.interpro_ac "
                            . "FROM   protein_feature pf "
                            . "LEFT JOIN interpro AS i ON pf.hit_name = i.id "
                            . "LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac "
                            . "WHERE  pf.protein_feature_id = ?";
 
  my $sth = $self->prepare($select_sql);
 
  $sth->bind_param(1, $protfeat_id, SQL_INTEGER);
  my $res = $sth->execute();
 
  my $pf_hash_ref = $sth->fetchrow_hashref();
 
  if($sth->rows == 0) {
    $sth->finish();
    return undef;
  }
 
  $sth->finish();
 
  my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_dbID($pf_hash_ref->{analysis_id});
 
  my( $cigar_string, $align_type);
  $cigar_string = $pf_hash_ref->{cigar_line} if exists $pf_hash_ref->{cigar_line}; # available > e92
  $align_type = $pf_hash_ref->{align_type} if exists $pf_hash_ref->{align_type}; # available > e92
 
 
  return
    Bio::EnsEMBL::ProteinFeature->new(-ADAPTOR     => $self,
                                      -DBID        => $protfeat_id,
                                      -START       => $pf_hash_ref->{seq_start},
                                      -END         => $pf_hash_ref->{seq_end},
                                      -HSTART      => $pf_hash_ref->{hit_start},
                                      -HEND        => $pf_hash_ref->{hit_end},
                                      -HSEQNAME    => $pf_hash_ref->{hit_name},
                                      -HDESCRIPTION => $pf_hash_ref->{hit_description},
                                      -ANALYSIS    => $analysis,
                                      -SCORE       => $pf_hash_ref->{score},
                                      -P_VALUE     => $pf_hash_ref->{evalue},
                                      -PERCENT_ID  => $pf_hash_ref->{perc_ident},
                                      -IDESC       => $pf_hash_ref->{description},
                                      -ILABEL      => $pf_hash_ref->{display_label},
                                      -INTERPRO_AC => $pf_hash_ref->{interpro_ac},
                                      -TRANSLATION_ID  => $pf_hash_ref->{translation_id},
                                      -CIGAR_STRING => $cigar_string,
                                      -ALIGN_TYPE => $align_type
                                      );
} ## end sub fetch_by_dbID

◆ fetch_Iterator_by_Slice()

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

Undocumented method

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◆ fetch_Iterator_by_Slice_method()

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

Undocumented method

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◆ get_seq_region_id_external()

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

Undocumented method

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◆ get_seq_region_id_internal()

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

Undocumented method

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◆ remove_by_Slice()

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

Undocumented method

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◆ store()

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

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sub store {
  my ($self, $feature, $translation_id) = @_;
 
  if (!ref($feature) || !$feature->isa('Bio::EnsEMBL::ProteinFeature')) {
    throw("ProteinFeature argument is required");
  }
 
  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 $insert_ignore = $self->insert_ignore_clause();
  my @insert_cols = $self->_tbl_columns(1);  # skip pk - protein_feature_id
 
  my @insert_values = map { '?' } @insert_cols;
  my $insert_stmt = "${insert_ignore} INTO protein_feature (". (join ',', @insert_cols) .  ') VALUES (' . (join ',',  @insert_values) . ')';
 
  my $sth = $self->prepare($insert_stmt);
 
  my $i = 0;
  $sth->bind_param(++$i, $translation_id,        SQL_INTEGER);
  $sth->bind_param(++$i, $feature->start,        SQL_INTEGER);
  $sth->bind_param(++$i, $feature->end,          SQL_INTEGER);
  $sth->bind_param(++$i, $feature->hstart,       SQL_INTEGER);
  $sth->bind_param(++$i, $feature->hend,         SQL_INTEGER);
  $sth->bind_param(++$i, $feature->hseqname,     SQL_VARCHAR);
  $sth->bind_param(++$i, $analysis->dbID,        SQL_INTEGER);
  $sth->bind_param(++$i, $feature->score,        SQL_DOUBLE);
  $sth->bind_param(++$i, $feature->p_value,      SQL_DOUBLE);
  $sth->bind_param(++$i, $feature->percent_id,   SQL_FLOAT);
  $sth->bind_param(++$i, $feature->external_data,      SQL_VARCHAR);
  $sth->bind_param(++$i, $feature->hdescription, SQL_LONGVARCHAR);
 
  if ($self->schema_version > 92) {
    $sth->bind_param(++$i, $feature->cigar_string,      SQL_VARCHAR);
    $sth->bind_param(++$i, $feature->align_type,      SQL_VARCHAR);
  }
 
  $sth->execute();
 
  if (defined($sth->err) && $sth->err eq 0){ # is a warning if 0 and defined
      warning('SQL warning : ' . $sth->errstr ."\n");
  }
 
  my $dbID = $self->last_insert_id('protein_feature_id', undef, 'protein_feature');
 
  $feature->adaptor($self);
  $feature->dbID($dbID);
 
  $sth->finish();
 
  return $dbID;
} ## end sub store

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

ensembl/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm

Public Member Functions

Detailed Description

Synopsis

Member Function Documentation

◆ _columns()

◆ _left_join()

◆ _objs_from_sth()

◆ _tables()

◆ _tbl_columns()

◆ count_by_Slice_constraint()

◆ fetch_all_by_logic_name()

◆ fetch_all_by_Slice()

◆ fetch_all_by_Slice_and_external_db()

◆ fetch_all_by_Slice_and_hcoverage()

◆ fetch_all_by_Slice_and_pid()

◆ fetch_all_by_Slice_and_score()

◆ fetch_all_by_Slice_constraint()

◆ fetch_all_by_stable_id_list()

◆ fetch_all_by_translation_id()

◆ fetch_all_by_uniprot_acc()

◆ fetch_by_dbID()

◆ fetch_Iterator_by_Slice()

◆ fetch_Iterator_by_Slice_method()

◆ get_seq_region_id_external()

◆ get_seq_region_id_internal()

◆ remove_by_Slice()

◆ store()