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Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor:

List of all members.


Class Summary

Definition at line 10 of file ConstrainedElementAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected _fetch_all_ConstrainedElements ()
protected _fetch_all_ConstrainedElements_by_dbID ()
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 void delete_by_dbID ()
public void delete_by_MethodLinkSpeciesSet ()
public dump_data ()
public fetch_all ()
public Listref fetch_all_by_dbID ()
public Listref fetch_all_by_dbID_list ()
public Listref fetch_all_by_MethodLinkSpeciesSet_Dnafrag ()
public Listref fetch_all_by_MethodLinkSpeciesSet_Slice ()
public
Bio::EnsEMBL::Compara::ConstrainedElement 
fetch_by_dbID ()
public Listref generic_fetch ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public void store ()

Method Documentation

protected Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::_fetch_all_ConstrainedElements ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::_fetch_all_ConstrainedElements_by_dbID ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::delete_by_dbID ( )
  Arg  1     : int $constrained_element_id
  Example    : $constrained_element_adaptor->delete_by_dbID(123);
  Description: It removes constrained elements with the specified ID
  Returntype : none
  Exceptions : none
  Caller     : general
 
Code:
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public void Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::delete_by_MethodLinkSpeciesSet ( )
  Arg  1     : method_link_species_set object $mlss
  Example    : $constrained_element_adaptor->delete_by_MethodLinkSpeciesSet($mlss);
  Description: It removes constrained elements with the specified method_link_species_set_id from the database
  Returntype : none
  Exceptions : throw if passed parameter is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object 
  Caller     : general
 
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public Listref Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::fetch_all_by_dbID ( )
  Arg  1     : listref of constrained_element_ids
  Example    : my $listref_of_constrained_elements = $constrained_element_adaptor->fetch_all_by_dbID($list_ref_of_constrained_element_ids);
  Description: Retrieve the corresponding constrained_elements from a given list of constrained_element_ids 
  Returntype : listref of Bio::EnsEMBL::Compara::ConstrainedElement constrained_elements 
  Exceptions : throw if Arg-1 is not a listref
  Caller     : object::methodname
 
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public Listref Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::fetch_all_by_MethodLinkSpeciesSet_Dnafrag ( )
  Arg  1     : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet mlss_obj
  Arg  2     : Bio::EnsEMBL::Compara::DnaFrag dnafrag_obj
  Example    : my $listref_of_constrained_elements = $constrained_element_adaptor->
  		fetch_all_by_MethodLinkSpeciesSet_Dnafrag($mlss_obj, $dnafrag_obj);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::ConstrainedElement object listref
  Returntype : listref of Bio::EnsEMBL::Compara::ConstrainedElement objects
  Exceptions : throw if Arg-1 is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet mlss_obj object
	       throw if Arg-2 is not a Bio::EnsEMBL::Compara::DnaFrag object
  Caller     : object::methodname
 
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public Listref Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::fetch_all_by_MethodLinkSpeciesSet_Slice ( )
  Arg  1     : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss_obj
  Arg  2     : Bio::EnsEMBL::Slice $slice_obj
  Example    : my $listref_of_constrained_elements = $constrained_element_adaptor->
  		fetch_all_by_MethodLinkSpeciesSet_Slice($mlss_obj, $slice_obj);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::ConstrainedElement object listref
  Returntype : listref of Bio::EnsEMBL::Compara::ConstrainedElement objects
  Exceptions : throw if Arg-1 is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
	       throw if Arg-2 is not a Bio::EnsEMBL::Slice object
  Caller     : object::methodname
 
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public Bio::EnsEMBL::Compara::ConstrainedElement Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::fetch_by_dbID ( )
  Arg  1     : int constrained_element_id
  Example    : my $constrained_element = $constrained_element_adaptor->
               fetch_by_dbID($constrained_element_id);
  Description: Retrieve the corresponding constrained_element.
  Returntype : Bio::EnsEMBL::Compara::ConstrainedElement object
  Exceptions : -none-
  Caller     : object::methodname
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::new ( )

Undocumented method

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

public void Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor::store ( )
  Arg  1     : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object 
  Arg  2     : listref of Bio::EnsEMBL::Compara::ConstrainedElement ($constrained_element) objects 
               The things you want to store
  Example    : none
  Description: It stores the given ConstrainedElements in the database.
  Returntype : none
  Exceptions : throw if Arg-1 is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
	       throw if Arg-2 is not a Bio::EnsEMBL::Compara::ConstrainedElement	
  Caller     : called by the Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp module
 
Code:
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The documentation for this class was generated from the following file: