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

List of all members.


Class Summary

Definition at line 8 of file SpeciesSetAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected void _delete_tagvalue ()
protected _final_clause ()
protected _left_join ()
protected _list_dbIDs ()
protected void _load_tagvalues ()
protected _objs_from_sth ()
protected void _read_attr_list ()
protected void _store_tagvalue ()
protected _straight_join ()
protected _tables ()
protected _tag_capabilities ()
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 fetch_all_by_GenomeDBs ()
public Listref fetch_all_by_tag ()
public
Bio::EnsEMBL::Compara::SpeciesSet 
fetch_all_by_tag_value ()
public
Bio::EnsEMBL::Compara::SpeciesSet 
fetch_by_dbID ()
public
Bio::EnsEMBL::Compara::SpeciesSet 
fetch_by_GenomeDBs ()
public Listref generic_fetch ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public void new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public
Bio::EnsEMBL::Compara::SpeciesSet 
store ()
public void sync_tags_to_database ()

Method Documentation

protected void Bio::EnsEMBL::Compara::DBSQL::TagAdaptor::_delete_tagvalue ( ) [inherited]
  Description: removes a tag from the database
  Arg [1]    : <scalar> object
  Arg [2]    : <string> tag
  Arg [3]    : (optional) <string> value
  Example    : $speciesset_adaptor->_delete_tagvalue($species_set, "colour");
  Returntype : none
  Exceptions : none
  Caller     : internal
 
Code:
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protected void Bio::EnsEMBL::Compara::DBSQL::TagAdaptor::_load_tagvalues ( ) [inherited]
  Description: retrieves all the tags and attributes from the database and
               calls add_tag to store them in the PERL hash
  Arg [1]    : <scalar> reference object
  Example    : $genetree_adaptor->_load_tagvalues($tree);
  Returntype : none
  Exceptions : none
  Caller     : internal
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor.

protected void Bio::EnsEMBL::Compara::DBSQL::TagAdaptor::_read_attr_list ( ) [inherited]
  Description: retrieves the column names of an attribute table
  Arg [1]    : <scalar> table name
  Example    : $genetree_adaptor->_read_attr_list('protein_tree_node_attr');
  Returntype : none
  Exceptions : none
  Caller     : internal
 
Code:
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protected void Bio::EnsEMBL::Compara::DBSQL::TagAdaptor::_store_tagvalue ( ) [inherited]
  Arg [1]    : <scalar> object
  Arg [2]    : <string> tag
  Arg [3]    : <string> value
  Arg [4]    : (optional) <int> allows overloading the tag with different values
               default is 0 (no overloading allowed, one tag points to one value)
  Example    : $speciesset_adaptor->_store_tagvalue($species_set, "colour", "red");
  Returntype : none
  Exceptions : none
  Caller     : internal
 
Code:
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protected Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor::_tag_capabilities ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::TagAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor::fetch_all ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor::fetch_all_by_GenomeDBs ( )

Undocumented method

Code:
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public Listref Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor::fetch_all_by_tag ( )
  Arg [1]     : string $tag
  Example     : my $species_sets = $species_set_adaptor->fetch_all_by_tag("taxon_id");
  Description : Fetches the SpeciesSet object that have this tag
  Returntype  : listref of Bio::EnsEMBL::Compara::SpeciesSet objects
  Exceptions  : None
  Caller      : general
  Status      : Stable
 
Code:
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public Bio::EnsEMBL::Compara::SpeciesSet Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor::fetch_all_by_tag_value ( )
  Arg [1]     : string $tag
  Arg [2]     : string $value
  Example     : my $species_set = $species_set_adaptor->fetch_by_tag_value("name", "primates");
  Description : Fetches the SpeciesSet object with that tag-value pair. If more than one
                species_set exists with this tag-value pair, returns the species_set
                with the largest species_set_id
  Returntype  : Bio::EnsEMBL::Compara::SpeciesSet
  Exceptions  : None
  Caller      : general
  Status      : Stable
 
Code:
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public Bio::EnsEMBL::Compara::SpeciesSet Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor::fetch_by_dbID ( )
  Arg [1]     : int $species_set_id
  Example     : my $species_set = $species_set_adaptor->fetch_by_dbID($species_set_id);
  Description : Fetches the SpeciesSet object with that internal ID
  Returntype  : Bio::EnsEMBL::Compara::SpeciesSet
  Exceptions  : None
  Caller      : general
  Status      : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::SpeciesSet Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor::fetch_by_GenomeDBs ( )
  Arg [1]     : listref of Bio::EnsEMBL::Compara::GenomeDB objects
  Example     : my $species_set = $species_set_adaptor->fetch_by_GenomeDBs($genome_dbs);
  Description : Fetches the SpeciesSet object for that set of GenomeDBs
  Returntype  : Bio::EnsEMBL::Compara::SpeciesSet
  Exceptions  : thrown if a GenomeDB has no dbID. Warns if more than one SpeciesSet has
                this set of GenomeDBs
  Caller      : general
  Status      : Stable
 
Code:
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public void Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor::new ( )
  Arg [1]    : list of args to super class constructor
  Example    : $ga_a = new Bio::EnsEMBL::Compara::SpeciesSetAdaptor($dbobj);
  Description: Creates a new SpeciesSetAdaptor.  This
               class should be instantiated through the get method on the 
               DBAdaptor rather than calling this method directly.
  Returntype : none
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBConnection
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::SpeciesSet Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor::store ( )
  Arg [1]     : Bio::EnsEMBL::Compara::SpeciesSet object
  Example     : my $species_set = $species_set_adaptor->store($species_set);
  Description : Stores the object in the database. Checks that all the
                Bio::EnsEMBL::Compara::GenomeDB objects in the genome_dbs
                array have a dbID. Assigns a species_set_id if the object hasn't
                got one (this locks the table). Also stores the tags if any
  Returntype  : Bio::EnsEMBL::Compara::SpeciesSet
  Exceptions  : thrown if a GenomeDB has no dbID
  Caller      : general
  Status      : Stable
 
Code:
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public void Bio::EnsEMBL::Compara::DBSQL::TagAdaptor::sync_tags_to_database ( ) [inherited]
  Description: rewrites all the tags from memory to the database
  Arg [1]    : <scalar> object
  Example    : $speciesset_adaptor->sync_tags_to_database($species_set);
  Returntype : none
  Exceptions : none
  Caller     : general
 
Code:
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The documentation for this class was generated from the following file: