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

List of all members.


Class Summary

Synopsis

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

Description

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

Definition at line 24 of file OperonAdaptor.pm.

Available Methods

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

Method Documentation

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

Undocumented method

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

Undocumented method

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

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

Undocumented method

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

Undocumented method

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

Undocumented method

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Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, and Bio::EnsEMBL::DBSQL::PredictionExonAdaptor.

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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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

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

Undocumented method

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

Undocumented method

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

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

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

Deprecated:
use fetch_all_by_Slice instead
 
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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
 
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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_constraint ( ) [inherited]
  Description:

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

public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_and_score ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) float $score
               lower bound of the the score of the features retrieved
  Arg [3]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Example    : $fts = $a->fetch_all_by_Slice_and_score($slice,90,'Swall');
  Description: Returns a list of features created from the database which are 
               are on the Slice defined by $slice and which have a score 
               greater than $score. If $logic_name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
  Exceptions : none
  Caller     : Bio::EnsEMBL::Slice
  Status     : Stable
 
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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
 
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public Listref Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_all_versions_by_stable_id ( )
  Arg [1]     : String $stable_id 
                The stable ID of the operon to retrieve
  Example     : $operon = $operon_adaptor->fetch_all_versions_by_stable_id
                  ('ENSG00000148944');
  Description : Similar to fetch_by_stable_id, but retrieves all versions of a
                operon stored in the database.
  Returntype  : listref of Bio::EnsEMBL::Operon
  Exceptions  : if we cant get the operon in given coord system
  Caller      : general
  Status      : At Risk
 
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public Bio::EnsEMBL::Feature Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_by_dbID ( ) [inherited]
  Arg [1]    : int $id
               The unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234));
               $feat = $feat->transform('contig');
  Description: Returns the feature created from the database defined by the
               the id $id.  The feature will be returned in its native
               coordinate system.  That is, the coordinate system in which it
               is stored in the database.  In order to convert it to a
               particular coordinate system use the transfer() or transform()
               method.  If the feature is not found in the database then
               undef is returned instead
  Returntype : Bio::EnsEMBL::Feature or undef
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable
 
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Reimplemented in Bio::EnsEMBL::DBSQL::AnalysisAdaptor, Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor, Bio::EnsEMBL::DBSQL::CoordSystemAdaptor, Bio::EnsEMBL::DBSQL::DBEntryAdaptor, Bio::EnsEMBL::DBSQL::DensityTypeAdaptor, Bio::EnsEMBL::DBSQL::MiscSetAdaptor, Bio::EnsEMBL::DBSQL::OntologyTermAdaptor, Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor, Bio::EnsEMBL::DBSQL::TranslationAdaptor, Bio::EnsEMBL::Map::DBSQL::DitagAdaptor, Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlAdaptor.

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

Undocumented method

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

Undocumented method

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public Bio::EnsEMBL::Operon Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_by_operon_transcript_stable_id ( )
  Arg [1]    : string $trans_stable_id
               transcript stable ID whose operon should be retrieved
  Example    : my $operon = $operon_adaptor->fetch_by_operon_transcript_stable_id
                 ('ENST0000234');
  Description: Retrieves a operon from the database via the stable ID of one of
               its transcripts
  Returntype : Bio::EnsEMBL::Operon
  Exceptions : none
  Caller     : operonral
  Status     : Stable
 
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public Bio::EnsEMBL::Operon Bio::EnsEMBL::DBSQL::OperonAdaptor::fetch_by_stable_id ( )
  Arg [1]    : String $id 
               The stable ID of the operon to retrieve
  Example    : $operon = $operon_adaptor->fetch_by_stable_id('ENSG00000148944');
  Description: Retrieves a operon object from the database via its stable id.
               The operon will be retrieved in its native coordinate system (i.e.
               in the coordinate system it is stored in the database). It may
               be converted to a different coordinate system through a call to
               transform() or transfer(). If the operon or exon is not found
               undef is returned instead.
  Returntype : Bio::EnsEMBL::Operon or undef
  Exceptions : if we cant get the operon in given coord system
  Caller     : general
  Status     : Stable
 
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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
 
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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
 
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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
 
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Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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public Reference Bio::EnsEMBL::DBSQL::OperonAdaptor::list_stable_ids ( )
  Example    : @stable_operon_ids = @{$operon_adaptor->list_stable_ids()};
  Description: Gets an listref of stable ids for all operons in the current db
  Returntype : reference to a list of strings
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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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
 
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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::OperonAdaptor::remove ( )
  Arg [1]    : Bio::EnsEMBL::Operon $operon
               the operon to remove from the database
  Example    : $operon_adaptor->remove($operon);
  Description: Removes a operon completely from the database. All associated
               transcripts, exons, stable_identifiers, descriptions, etc.
               are removed as well. Use with caution!
  Returntype : none
  Exceptions : throw on incorrect arguments 
               warning if operon is not stored in this database
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.

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

Undocumented method

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


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