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Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor:

List of all members.


Class Summary

Synopsis

  $db = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor-\>new(...);

  $vsa = $db-\>get_VariationSetAdaptor();

  # retrieve a variation set by its name
  $vs = $vsa-\>fetch_by_name('Phenotype-associated variations');

  # retrieve a variation set by its internal identifier
  $vs = $vsa-\>fetch_by_dbID(12);

  # retrieve all variation sets which a variation is a part of
  @vs = @{$vsa-\>fetch_all_by_Variation($var)};

Description

This adaptor provides database connectivity for VariationSet objects.
VariationSets may be retrieved from the Ensembl variation database by
several means using this module.
 

Definition at line 34 of file VariationSetAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected _final_clause ()
protected _get_bitvalue ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _short_name_attrib_type_code ()
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 Reference fetch_all_by_StructuralVariation ()
public Listref fetch_all_by_sub_VariationSet ()
public Listref fetch_all_by_super_VariationSet ()
public Reference fetch_all_by_Variation ()
public Istref fetch_all_top_VariationSets ()
public Bio::EnsEMBL::Feature fetch_by_dbID ()
public
Bio::EnsEMBL::Variation::VariationSet 
fetch_by_name ()
public
Bio::EnsEMBL::Variation::VariationSet 
fetch_by_short_name ()
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 Int species_id ()

Method Documentation

protected Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::_columns ( )

Undocumented method

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

protected Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::_default_where_clause ( )

Undocumented method

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

protected Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::_get_bitvalue ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::_objs_from_sth ( )

Undocumented method

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

protected Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::_short_name_attrib_type_code ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::_tables ( )

Undocumented method

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

public Reference Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::fetch_all_by_StructuralVariation ( )
  Arg [1]    : Bio::EnsEMBL::Variation::StructuralVariation
  Example    : my $vss = $vsa->fetch_all_by_StructuralVariation($sv);
  Description: Retrieves all variation sets which a particular structural variation
               is present in.
  Returntype : reference to list of Bio::EnsEMBL::Variation::VariationSets
  Exceptions : throw on incorrect argument
  Caller     : general
  Status     : At Risk
 
Code:
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public Listref Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::fetch_all_by_sub_VariationSet ( )
  Arg [1]    : Bio::EnsEMBL::Variation::VariationSet $sub
  Arg [2]    : (optional) boolean $only_immediate
               If true, only the direct supersets of this variation set will be fetched. The default behaviour is
               to recursively fetch all supersets.
  Example    : @vs_supersets = @{$vs_adaptor->fetch_all_by_sub_VariationSet($vs)};
  Description: Retrieves all VariationSets that are direct supersets of the specified VariationSet.
  Returntype : listref of Bio::EnsEMBL::Variation::VariationSet
  Exceptions : throw if sub arg is not valid
  Caller     : general
  Status     : At Risk
 
Code:
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public Listref Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::fetch_all_by_super_VariationSet ( )
  Arg [1]    : Bio::EnsEMBL::Variation::VariationSet $super
  Arg [2]    : (optional) boolean $only_immediate
               If true, only the direct subsets of this variation set will be fetched. The default behaviour is
               to recursively fetch all subsets.
  Example    : @vs_subsets = @{$vs_adaptor->fetch_all_by_super_VariationSet($vs)};
  Description: Retrieves all VariationSets that are subsets of the specified VariationSet.
  Returntype : listref of Bio::EnsEMBL::Variation::VariationSet
  Exceptions : throw if super arg is not valid
  Caller     : general
  Status     : At Risk
 
Code:
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public Reference Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::fetch_all_by_Variation ( )
  Arg [1]    : Bio::EnsEMBL::Variation::Variation
  Example    : my $vgs = $vga->fetch_all_by_Variation($var);
  Description: Retrieves all variation sets which a particular variation
               is present in.
  Returntype : reference to list of Bio::EnsEMBL::Variation::VariationSets
  Exceptions : throw on incorrect argument
  Caller     : general
  Status     : At Risk
 
Code:
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public Istref Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::fetch_all_top_VariationSets ( )
  Example    : $vs = $vs_adaptor->fetch_all_top_VariationSets();
  Description: Retrieves all VariationSet objects that are 'toplevel', 
               i.e. they are not subsets of any other variation set.
  Returntype : istref of Bio::EnsEMBL::Variation::VariationSet
  Exceptions : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Bio::EnsEMBL::Variation::VariationSet Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::fetch_by_name ( )
  Arg [1]    : string $name
  Example    : $vg = $vga->fetch_by_name('Phenotype-associated variations');
  Description: Retrieves a variation set by its name.
  Returntype : Bio::EnsEMBL::Variation::VariationSet
  Exceptions : throw if name argument is not provided
  Caller     : general
  Status     : At Risk
 
Code:
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public Bio::EnsEMBL::Variation::VariationSet Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor::fetch_by_short_name ( )
  Arg [1]    : string $name
  Example    : $vg = $vga->fetch_by_short_name('ph_variants');
  Description: Retrieves a variation set by its short name.
  Returntype : Bio::EnsEMBL::Variation::VariationSet
  Exceptions : throw if short name argument is not provided
  Caller     : general
 
Code:
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The documentation for this class was generated from the following file: