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

List of all members.


Class Summary

Synopsis

  my $uoa = $database_adaptor-\>get_UnmappedObjectAdaptor();

  my $missed = @{ $uoa-\>fetch_all_by_type('xref') };

Description

Unmapped ObjectAdaptor - An adaptor responsible for the creation,
editing, retrieval of Unmapped Objects. These being the Objects that
where not mapped in a specific process i.e. xref, cDNA, Markers.
 

Definition at line 25 of file UnmappedObjectAdaptor.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 fetch_all ()
public Array fetch_all_by_analysis ()
public Listref fetch_all_by_dbID_list ()
public Listref fetch_all_by_logic_name ()
public Array fetch_all_by_object_type_id ()
public fetch_all_by_RawContig ()
public fetch_all_by_RawContig_and_score ()
public fetch_all_by_RawContig_constraint ()
public Listref fetch_all_by_Slice ()
public Listref fetch_all_by_Slice_and_score ()
public Listref fetch_all_by_Slice_constraint ()
public Array fetch_all_by_type ()
public Bio::EnsEMBL::Feature fetch_by_dbID ()
public Array fetch_by_identifier ()
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 List list_dbIDs ()
public List list_unmapped_reasons ()
public
Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor 
new ()
public DBI::StatementHandle prepare ()
public void remove ()
public remove_by_analysis_id ()
public remove_by_feature_id ()
public remove_by_RawContig ()
public void remove_by_Slice ()
public Int species_id ()
public Boolean start_equals_end ()
public void store ()

Method Documentation

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

Undocumented method

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protected Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::_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

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

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

Undocumented method

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

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::UnmappedObjectAdaptor::_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::UnmappedObjectAdaptor::_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 Array Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::fetch_all_by_analysis ( )
  Arg [1]  : Bio:EnsEMBL::Analysis object
  Arg [2]  : (optional) string database name
  Example  : @unmapped_object = @{$uoa->fetch_all_by_analysis($analysis)};
  Description : Retrieves all the unmapped object for a particular
                analysis type with the the option of a particular
                database type.
  Returntype  : array ref of Bio::EnsEMBL::UnmappedObject
  Exceptions  : thorws if first argument is not an anaylisi object
  Caller      : general
  Status      : At Risk
 
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public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all_by_dbID_list ( ) [inherited]
  Arg [1]    : listref of integers $id_list
               The unique database identifiers for the features to
               be obtained.
  Arg [2]    : optional - Bio::EnsEMBL::Slice to map features onto.
  Example    : @feats = @{$adaptor->fetch_all_by_dbID_list([1234, 2131, 982]))};
  Description: Returns the features created from the database
               defined by the the IDs in contained in the provided
               ID list $id_list.  The features will be returned
               in their native coordinate system.  That is, the
               coordinate system in which they are stored in the
               database.  In order to convert the features to a
               particular coordinate system use the transfer() or
               transform() method.  If none of the features are
               found in the database a reference to an empty list is
               returned.
  Returntype : listref of Bio::EnsEMBL::Features
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.

public Listref Bio::EnsEMBL::DBSQL::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 Array Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::fetch_all_by_object_type_id ( )
  Arg [1]  : string - The object type of the ensembl object e.g. Gene
  Arg [2]  : int    - The internal dbID of the ensembl object
  Example  : my @unmapped_objects = @{$uoa->fetch_all_by_object_type_id('Gene', 12341)};
  Description : Retrieves the unmapped objects for a particular ensembl object
                This is a base method which should be called by wrapper methods
                defining the correct object type e.g. $uoa->fetch_all_by_Gene($gene)
  Returntype  : array ref of Bio::EnsEMBL::UnmappedObject objects
  Exceptions  : Throws if arguments are not defined
  Caller      : general
  Status      : At Risk
 
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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig ( ) [inherited]
  Description:

Deprecated:
use fetch_all_by_Slice instead
 
Code:
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public Bio::EnsEMBL::DBSQL::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 Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Example    : $fts = $a->fetch_all_by_Slice($slice, 'Swall');
  Description: Returns a listref of features created from the database 
               which are on the Slice defined by $slice. If $logic_name is 
               defined only features with an analysis of type $logic_name 
               will be returned. 
               NOTE: only features that are entirely on the slice's seq_region
               will be returned (i.e. if they hang off the start/end of a
               seq_region they will be discarded). Features can extend over the
               slice boundaries though (in cases where you have a slice that
               doesn't span the whole seq_region).
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
  Exceptions : none
  Caller     : Bio::EnsEMBL::Slice
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventAdaptor, and Bio::EnsEMBL::DBSQL::TranscriptAdaptor.

public Listref Bio::EnsEMBL::DBSQL::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 Array Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::fetch_all_by_type ( )
  Arg [1]  : string type. The type of unmapped objects
  Example  : @unmapped_object = @{$uoa->fetch_all_by_type('xref')};
  Description : Retrieves all the unmapped object for a particular
                type. e.g. 'xref','cDNA', 'marker'
  Returntype  : Array ref of Bio::EnsEMBL::UnmappedObject
  Exceptions  : none
  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 Array Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::fetch_by_identifier ( )
  Arg [1]  : string type. The type of unmapped objects
  Arg [2]  : (optional) string database name
  Example  : @unmapped_object = @{$uoa->fetch_by_identifier('Q123345')};
  Description : Retrieves the unmapped object for a particular
                identifier/accession
  Returntype  : array ref of Bio::EnsEMBL::UnmappedObject
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
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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 List Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::list_dbIDs ( )
  Arg [1]    : none
  Example    : @unmapped_object_ids = @{$unmapped_object_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all unmapped_objects in the current db
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable
 
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public List Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::list_unmapped_reasons ( )
  Arg [1]    : none
  Example    : @unmapped_object_reason+ids = 
                   @{$unmapped_object_adaptor->list_unmapped_reasons()};
  Description: Gets an array of internal ids for all unmapped_objects in the current db
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable
 
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public Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::new ( )
  Arg [1]    : list of args @args
               Superclass constructor arguments
  Example    : none
  Description: Constructor which just initializes internal cache structures
  Returntype : Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor
  Exceptions : none
  Caller     : implementing subclass constructors
  Status     : At Risk
 
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.

public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare ( ) [inherited]
  Arg [1]    : string $string
               a SQL query to be prepared by this adaptors database
  Example    : $sth = $adaptor->prepare("select yadda from blabla")
  Description: provides a DBI statement handle from the adaptor. A convenience
               function so you dont have to write $adaptor->db->prepare all the
               time
  Returntype : DBI::StatementHandle
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::DBSQL::SliceAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

public void Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove ( ) [inherited]
  Arg [1]    : A feature $feature 
  Example    : $feature_adaptor->remove($feature);
  Description: This removes a feature from the database.  The table the
               feature is removed from is defined by the abstract method
               _tablename, and the primary key of the table is assumed
               to be _tablename() . '_id'.  The feature argument must 
               be an object implementing the dbID method, and for the
               feature to be removed from the database a dbID value must
               be returned.
  Returntype : none
  Exceptions : thrown if $feature arg does not implement dbID(), or if
               $feature->dbID is not a true value
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::PredictionExonAdaptor, Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor, and Bio::EnsEMBL::DBSQL::TranscriptAdaptor.

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

Undocumented method

Code:
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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_feature_id ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_RawContig ( ) [inherited]
  Description:

Deprecated:
use remove_by_Slice instead
 
Code:
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public void Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_Slice ( ) [inherited]
  Arg [1]    : Bio::Ensembl::Slice $slice
  Example    : $feature_adaptor->remove_by_Slice($slice);
  Description: This removes features from the database which lie on a region
               represented by the passed in slice.  Only features which are
               fully contained by the slice are deleted; features which overlap
               the edge of the slice are not removed.
               The table the features are removed from is defined by
               the abstract method_tablename.
  Returntype : none
  Exceptions : thrown if no slice is supplied
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id ( ) [inherited]
  Arg [1]    : (optional) int $species_id
               The internal ID of the species in a multi-species database.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the internal ID of the species in a
               multi-species database.  The default species ID is 1.
  Returntype : Integer
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable
 
Code:
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public Boolean Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::start_equals_end ( ) [inherited]
  Arg [1]    : (optional) boolean $newval
  Example    : $bfa->start_equals_end(1);
  Description: Getter/Setter for the start_equals_end flag.  If set
               to true sub _slice_fetch will use a simplified sql to retrieve 1bp slices.
  Returntype : boolean
  Exceptions : none
  Caller     : EnsemblGenomes variation DB build
  Status     : Stable
 
Code:
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public void Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::store ( )
  Arg [1]    : list of Bio::EnsEMBL::UnmappedObjects @uo
               the unmapped objects to store in the database
  Example    : $ou_adaptor->store(@uo);
  Description: Stores a list of unmapped objects in the database
  Returntype : none
  Exceptions : thrown if no Analysis, or no list of objects to store. 
  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: