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

List of all members.


Class Summary

Description

 

Synopsis

Description

 

Definition at line 17 of file NCBITaxonAdaptor.pm.

Available Methods

protected _build_tree_from_nodes ()
protected _columns ()
protected _construct_sql_query ()
protected _default_where_clause ()
protected void _delete_tagvalue ()
protected _final_clause ()
protected Listref _generic_fetch ()
protected _get_starting_lr_index ()
protected _left_join ()
protected _list_dbIDs ()
protected _load_tagvalues ()
protected _lr_table_name ()
protected _objs_from_sth ()
protected void _read_attr_list ()
protected void _store_tagvalue ()
protected _straight_join ()
protected _tables ()
protected Array _tag_capabilities ()
public Listref bind_param_generic_fetch ()
public cache_add_object ()
public cache_fetch_by_id ()
public clear_cache ()
public columns ()
public create_instance_from_rowhash ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public default_where_clause ()
public DESTROY ()
public dump_data ()
public Arrayref fetch_all ()
public Listref fetch_all_by_dbID_list ()
public fetch_all_children_for_node ()
public fetch_all_leaves_indexed ()
public fetch_all_roots ()
public Bio::EnsEMBL::Feature fetch_by_dbID ()
public
Bio::EnsEMBL::Compara::NestedSet 
fetch_first_shared_ancestor_indexed ()
public
Bio::EnsEMBL::Compara::NCBITaxon 
fetch_node_by_genome_db_id ()
public
Bio::EnsEMBL::Compara::NCBITaxon 
fetch_node_by_name ()
public fetch_node_by_node_id ()
public
Bio::EnsEMBL::Compara::NCBITaxon 
fetch_node_by_taxon_id ()
public fetch_node_id_by_merged_taxon_id ()
public Undef fetch_parent_for_node ()
public
Bio::EnsEMBL::Compara::NestedSet 
fetch_root_by_node ()
public fetch_subroot_by_left_right_index ()
public fetch_subtree_under_node ()
public fetch_tree_at_node_id ()
public final_clause ()
public Listref generic_fetch ()
public get_dumped_data ()
public init_instance_from_rowhash ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public left_join_clause ()
public new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public store ()
public void sync_tags_to_database ()
public Nothing sync_tree_leftright_index ()
public tables ()
public update ()
public update_subtree ()

Method Documentation

protected Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_build_tree_from_nodes ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_construct_sql_query ( ) [inherited]

Undocumented method

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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
 
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protected Listref Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_generic_fetch ( ) [inherited]
  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  Example    : $fts = $a->_generic_fetch('WHERE 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
 
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protected Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_get_starting_lr_index ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::CAFETreeAdaptor, and Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor.

protected Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::_load_tagvalues ( )

Undocumented method

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

protected Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::_lr_table_name ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::_objs_from_sth ( )

Undocumented method

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

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
 
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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
 
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protected Array Bio::EnsEMBL::Compara::DBSQL::TagAdaptor::_tag_capabilities ( ) [inherited]
  Description: returns the tag/attributes capabilities for the object. The
               return value is an array with 4 entries:

  • the name of the table to store tag
  • the name of the table to store attribute
  • the name of the key column in the tables
  • the name of the perl method to have the key value Arg [1] : <scalar> reference object Example : return ("species_set_tag", undef, "species_set_id", "dbID"); Returntype : Array of 4 entries Exceptions : none Caller : internal
 
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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor, Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor, and Bio::EnsEMBL::Compara::DBSQL::SpeciesSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::cache_add_object ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::cache_fetch_by_id ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::clear_cache ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::columns ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::create_instance_from_rowhash ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::default_where_clause ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::DESTROY ( ) [inherited]

Undocumented method

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public Arrayref Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_all ( ) [inherited]
  Arg[1]     : -none-
  Example    : $all_trees = $proteintree_adaptor->fetch_all();
  Description: Fetches from the database all the nested sets.
  Returntype : arrayref of Bio::EnsEMBL::Compara::NestedSet
  Exceptions :
  Caller     :
 
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

Reimplemented in Bio::EnsEMBL::Compara::DBSQL::CAFETreeAdaptor, and Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_all_children_for_node ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::CAFETreeAdaptor, and Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_all_leaves_indexed ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_all_roots ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor.

public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_first_shared_ancestor_indexed ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $node1
  Arg [2]    : Bio::EnsEMBL::Compara::NestedSet $node2
  Arg [n]    : Bio::EnsEMBL::Compara::NestedSet $node_n
  Example    : $lca = $nested_set_adaptor->fetch_first_shared_ancestor_indexed($node1, $node2);
  Description: Returns the first node of the tree that is an ancestor of all the nodes passed
               as arguments. There must be at least one argument, and all the nodes must share
               the same root
  Returntype : Bio::EnsEMBL::Compara::NestedSet
  Exceptions : thrown if the nodes don't share the same root_id
 
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public Bio::EnsEMBL::Compara::NCBITaxon Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::fetch_node_by_genome_db_id ( )
  Arg [1]    : a genome_db_id
  Example    : $taxon = $nbcitaxonDBA->fetch_node_by_genome_db_id($gdbID);
  Description: Returns an NCBITaxon object for the given genome_db_id.
  Returntype : Bio::EnsEMBL::Compara::NCBITaxon
  Exceptions : thrown if $gdbID is not defined
  Caller     : general
 
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public Bio::EnsEMBL::Compara::NCBITaxon Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::fetch_node_by_name ( )
  Arg [1]    : a taxonomy name
               the database name for a ncbi taxon
  Example    : $taxon = $nbcitaxonDBA->fetch_node_by_name($name);
  Description: Returns an NCBITaxon object for the given NCBI Taxon name.
  Returntype : Bio::EnsEMBL::Compara::NCBITaxon
  Exceptions : thrown if $name is not defined
  Caller     : general
 
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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_node_by_node_id ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor.

public Bio::EnsEMBL::Compara::NCBITaxon Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::fetch_node_by_taxon_id ( )
  Arg [1]    : int $taxon->dbID
               the database id for a ncbi taxon
  Example    : $taxon = $nbcitaxonDBA->fetch_node_by_taxon_id($taxon_id);
  Description: Returns an NCBITaxon object for the given NCBI Taxon id.
  Returntype : Bio::EnsEMBL::Compara::NCBITaxon
  Exceptions : thrown if $taxon_id is not defined
  Caller     : general
 
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public Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::fetch_node_id_by_merged_taxon_id ( )

Undocumented method

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public Undef Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::fetch_parent_for_node ( )
  Overview   : returns the parent NCBITaxon object for this node
  Example    : my $my_parent = $object->parent();
  Returntype : undef or Bio::EnsEMBL::Compara::NCBITaxon
  Exceptions : none
  Caller     : general
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_root_by_node ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $node
  Example    : $root = $nested_set_adaptor->fetch_root_by_node($node);
  Description: Returns the root of the tree for this node
               with links to all the intermediate nodes. Sister nodes
               are not included in the result. Use fetch_node_by_node_id()
               method to get the whole tree (loaded on demand)
  Returntype : Bio::EnsEMBL::Compara::NestedSet
  Exceptions : thrown if $node is not defined
  Status     : At-risk
  Caller     : $nested_set->root
 
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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_subroot_by_left_right_index ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_subtree_under_node ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_tree_at_node_id ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::final_clause ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::init_instance_from_rowhash ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::left_join_clause ( ) [inherited]
public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::new ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::store ( ) [inherited]
  Arg [1]    :
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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Reimplemented in Bio::EnsEMBL::Compara::DBSQL::CAFETreeAdaptor, Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor, and Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor.

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
 
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public Nothing Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::sync_tree_leftright_index ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $root
  Arg [2]    : Boolean; indicates if you wish to use a fresh database 
               connection to perform any locking. If you are within an existing
               transaction this is a good idea to avoid locking the LR table
               for the duration of your transaction
  Example    : $nsa->sync_tree_leftright_index($root);
  Description: For the given root this method looks for left right index
               offset recorded in lr_index_offset for the configured
               table. The program locks on this table to reserve a batch
               of identifiers which are then used to left_right index
               the tree.
               The left right indexing is called by this method on your given
               tree root
  Returntype : Nothing
  Exceptions : Only raised from DBI problems
  Caller     : Public
 
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public Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::tables ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor::update ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::update_subtree ( ) [inherited]

Undocumented method

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The documentation for this class was generated from the following file: