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

List of all members.


Class Summary

Synopsis

=head2 Retrieve data from the database

  my $method_link_species_sets = $mlssa-\>fetch_all;

  my $method_link_species_set = $mlssa-\>fetch_by_dbID(1);

  my $method_link_species_set = $mlssa-\>fetch_by_method_link_type_registry_aliases(
        "BLASTZ_NET", ["human", "Mus musculus"]);

  my $method_link_species_set = $mlssa-\>fetch_by_method_link_type_species_set_name(
        "EPO", "mammals")
  
  my $method_link_species_sets = $mlssa-\>fetch_all_by_method_link_type("BLASTZ_NET");

  my $method_link_species_sets = $mlssa-\>fetch_all_by_GenomeDB($genome_db);

  my $method_link_species_sets = $mlssa-\>fetch_all_by_method_link_type_GenomeDB(
        "PECAN", $gdb1);
  
  my $method_link_species_set = $mlssa-\>fetch_by_method_link_type_GenomeDBs(
        "TRANSLATED_BLAT", [$gdb1, $gdb2]);

=head2 Store/Delete data from the database

  $mlssa-\>store($method_link_species_set);

Description

This object is intended for accessing data in the method_link and method_link_species_set tables.
 

Definition at line 43 of file MethodLinkSpeciesSetAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected void _delete_tagvalue ()
protected _final_clause ()
protected String _get_method_link_class_from_id ()
protected HashRef _get_ml_attributes_from_ml_id ()
protected Int _get_species_set_id_from_genome_db_ids ()
protected Int _get_species_set_id_from_species_set ()
protected _left_join ()
protected _list_dbIDs ()
protected void _load_tagvalues ()
protected _objs_from_sth ()
protected void _read_attr_list ()
protected
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
_run_query_from_method_link_id_genome_db_ids ()
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 void delete ()
public dump_data ()
public Listref fetch_all ()
public Listref fetch_all_by_dbID_list ()
public fetch_all_by_genome_db_id ()
public Listref fetch_all_by_GenomeDB ()
public fetch_all_by_method_link_id ()
public fetch_all_by_method_link_id_genome_db_id ()
public fetch_all_by_method_link_id_GenomeDB ()
public Listref fetch_all_by_method_link_type ()
public fetch_all_by_method_link_type_genome_db_id ()
public Listref fetch_all_by_method_link_type_GenomeDB ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
fetch_by_dbID ()
public fetch_by_method_link_id_genome_db_ids ()
public fetch_by_method_link_id_GenomeDBs ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
fetch_by_method_link_type_genome_db_ids ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
fetch_by_method_link_type_GenomeDBs ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
fetch_by_method_link_type_registry_aliases ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
fetch_by_method_link_type_species_set_name ()
public Listref generic_fetch ()
public get_dumped_data ()
public Int get_max_alignment_length ()
public Int get_method_link_id_from_method_link_type ()
public String get_method_link_type_from_method_link_id ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
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 String Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::_get_method_link_class_from_id ( )
  Arg  1     : none
  Example    : my $method_link_class = $mlssa->_get_method_link_class_from_id()
  Description: Retrieve method_link_class corresponding to the method_link_id
  Returntype : string $method_link_class
  Exceptions : none
  Caller     :
 
protected HashRef Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::_get_ml_attributes_from_ml_id ( )
  Arg  1     : int $method_link_id
  Example    : my $values = $mlssa->_get_ml_values_from_ml_id(1)
  Description: Retrieve attributes for a given Method Link ID
  Returntype : HashRef keyed by type and class
  Exceptions : warns when no method_link matches the $method_link_id
  Caller     : Internal
 
Code:
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protected Int Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::_get_species_set_id_from_genome_db_ids ( )
  Arg  1     : listref of Bio::EnsEMBL::Compara::GenomeDB obejcts $species_set
  Example    : my $species_set_id = $mlssa->_get_species_set_id_from_species_set($mlss->species_set);
  Description: Retrieve species_set_id corresponding to this set of species
  Returntype : integer $species_set_id
  Exceptions :
  Caller     :
 
Code:
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protected Int Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::_get_species_set_id_from_species_set ( )
  Arg  1     : listref of Bio::EnsEMBL::Compara::GenomeDB obejcts $species_set
  Example    : my $species_set_id = $mlssa->_get_species_set_id_from_species_set($mlss->species_set);
  Description: Retrieve species_set_id corresponding to this set of species
  Returntype : integer $species_set_id
  Exceptions :
  Caller     :
 
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 Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::_run_query_from_method_link_id_genome_db_ids ( )
  Arg  1     : int $method_link_id
  Arg 2      : listref of int [$gdbid1, $gdbid2, $gdbid3]
  Example    : my $method_link_species_set =
                   $mlssa->_run_query_from_method_link_id_genome_db_ids(1,
                       [$human_genome_db->dbID,
                       $mouse_genome_db->dbID])
  Description: Retrieve the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
               corresponding to the given method_link_id and the given set of
               Bio::EnsEMBL::Compara::GenomeDB objects defined by the set of
               $genome_db_ids
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exceptions : Returns undef if no Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
               object is found
  Caller     :
 
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::MethodLinkSpeciesSetAdaptor::_tag_capabilities ( )

Undocumented method

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

public void Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::delete ( )
  Arg  1     : integer $method_link_species_set_id
  Example    : $mlssa->delete(23)
  Description: Deletes a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet entry from
               the database.
  Returntype : none
  Exception  :
  Caller     :
 
Code:
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public Listref Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all ( )
  Arg  1     : none
  Example    : my $method_link_species_sets = $mlssa->fetch_all
  Description: Retrieve all possible Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
               objects
  Returntype : listref of Bio::EnsEMBL::Compara::MethodLinkSpeciesSet objects
  Exceptions : none
  Caller     :
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_genome_db_id ( )
Deprecated:
: Use the fetch_all_by_GenomeDB methodsinstead
 
Code:
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public Listref Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_GenomeDB ( )
  Arg  1     : Bio::EnsEMBL::Compara::GenomeDB $genome_db
  Example    : my $method_link_species_sets = $mlssa->fetch_all_by_genome_db($genome_db)
  Description: Retrieve all the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet objects
               which includes the genome defined by the Bio::EnsEMBL::Compara::GenomeDB
               object or the genome_db_id in the species_set
  Returntype : listref of Bio::EnsEMBL::Compara::MethodLinkSpeciesSet objects
  Exceptions : wrong argument throws
  Caller     :
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_id ( )
Deprecated:
: Use the fetch_all_by_method_link_type method instead
 
public Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_id_genome_db_id ( )
Deprecated:
: Use the fetch_all_by_method_link_type_GenomeDB method instead
 
public Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_id_GenomeDB ( )
Deprecated:
: Use the fetch_all_by_method_link_type_GenomeDB method instead
 
public Listref Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_type ( )
  Arg  1     : string method_link_type
  Example    : my $method_link_species_sets =
                     $mlssa->fetch_all_by_method_link_type("BLASTZ_NET")
  Description: Retrieve all the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet objects
               corresponding to the given method_link_type
  Returntype : listref of Bio::EnsEMBL::Compara::MethodLinkSpeciesSet objects
  Exceptions : none
  Caller     :
 
public Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_type_genome_db_id ( )
Deprecated:
: Use the fetch_all_by_method_link_type_GenomeDB method instead
 
public Listref Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_type_GenomeDB ( )
  Arg  1     : string method_link_type
  Arg  2     : Bio::EnsEMBL::Compara::GenomeDB $genome_db
  Example    : my $method_link_species_sets =
                     $mlssa->fetch_all_by_method_link_type_GenomeDB("BLASTZ_NET", $rat_genome_db)
  Description: Retrieve all the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet objects
               corresponding to the given method_link_type and which include the
               given Bio::EnsEBML::Compara::GenomeDB
  Returntype : listref of Bio::EnsEMBL::Compara::MethodLinkSpeciesSet objects
  Exceptions : none
  Caller     :
 
public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_dbID ( )
  Arg  1     : integer $method_link_species_set_id
  Example    : my $method_link_species_set_id = $mlssa->fetch_by_dbID(1)
  Description: Retrieve the correspondig
               Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exceptions : Returns undef if no matching
               Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object can be retrieved
  Caller     : none
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_id_genome_db_ids ( )
Deprecated:
: Use the fetch_by_method_link_type_GenomeDBs method instead
 
public Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_id_GenomeDBs ( )
Deprecated:
: Use the fetch_by_method_link_type_GenomeDBs method instead!
 
public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_type_genome_db_ids ( )
  Arg  1     : string $method_link_type
  Arg 2      : listref of int [$gdbid1, $gdbid2, $gdbid3]
  Example    : my $method_link_species_set =
                   $mlssa->fetch_by_method_link_type_genome_db_id("MULTIZ",
                       [$human_genome_db->dbID,
                       $rat_genome_db->dbID,
                       $mouse_genome_db->dbID])
  Description: Retrieve the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
               corresponding to the given method_link and the given set of
               Bio::EnsEMBL::Compara::GenomeDB objects defined by the set of
               $genome_db_ids
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exceptions : Returns undef if no Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
               object is found
  Caller     :
 
public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_type_GenomeDBs ( )
  Arg  1     : string $method_link_type
  Arg 2      : listref of Bio::EnsEMBL::Compara::GenomeDB objects [$gdb1, $gdb2, $gdb3]
  Arg 3      : (optional) bool $no_warning
  Example    : my $method_link_species_set =
                   $mlssa->fetch_by_method_link_type_GenomeDBs("MULTIZ",
                       [$human_genome_db,
                       $rat_genome_db,
                       $mouse_genome_db])
  Description: Retrieve the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
               corresponding to the given method_link and the given set of
               Bio::EnsEMBL::Compara::GenomeDB objects
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exceptions : Returns undef if no Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
               object is found. It also send a warning message unless the
               $no_warning option is on
  Caller     :
 
public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_type_registry_aliases ( )
  Arg  1     : string $method_link_type
  Arg 2      : listref of core database aliases [$human, $mouse, $rat]
  Example    : my $method_link_species_set =
                   $mlssa->fetch_by_method_link_type_registry_aliases("MULTIZ",
                       ["human","mouse","rat"])
  Description: Retrieve the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
               corresponding to the given method_link and the given set of
               core database aliases defined in the Bio::EnsEMBL::Registry
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exceptions : Returns undef if no Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
               object is found
  Caller     :
 
public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_type_species_set_name ( )
  Arg  1     : string method_link_type
  Arg  2     : string species_set_name
  Example    : my $method_link_species_set =
                     $mlssa->fetch_by_method_link_type_species_set_name("EPO", "mammals")
  Description: Retrieve the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
               corresponding to the given method_link_type and and species_set_tag value
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exceptions : Returns undef if no Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
               object is found
  Caller     :
 
public Int Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::get_max_alignment_length ( )
  Arg 1      : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
  Example    :
  Description: Retrieve the maximum length for this type of alignments.
               This method is used for genomic (dna/dna) alignments only.
               This method sets and returns this attribute for this object
  Returntype : integer
  Exceptions :
  Caller     : Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor
 
Code:
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public Int Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::get_method_link_id_from_method_link_type ( )
  Arg  1     : string $method_link_type
  Example    : my $method_link_id = $mlssa->get_method_link_id_from_method_link_type("BLASTZ_NET")
  Description: Retrieve method_link_id corresponding to the method_link_type
  Returntype : integer $method_link_id
  Exceptions : warns when no method_link matches the $method_link_type
  Caller     :
 
public String Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::get_method_link_type_from_method_link_id ( )
  Arg  1     : none
  Example    : my $method_link_type = $mlssa->get_method_link_type_from_method_link_id()
  Description: Retrieve method_link_type corresponding to the method_link_id
  Returntype : string $method_link_type
  Exceptions : none
  Caller     :
 
public Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::new ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::store ( )
  Arg  1     : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Example    : $mlssa->store($method_link_species_set)
  Description: Stores a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object into
               the database if it does not exist yet. It also stores or updates
               accordingly the meta table if this object has a
               max_alignment_length attribute.
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exception  : Thrown if the argument is not a
               Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exception  : Thrown if the corresponding method_link is not in the
               database
  Caller     :
 
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: