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

List of all members.


Class Summary

Description

Specialization of Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor for non-coding genes
 

Definition at line 10 of file NCTreeAdaptor.pm.

Available Methods

protected _add_GeneTree_wrapper ()
protected _build_tree_from_nodes ()
protected _columns ()
protected _construct_sql_query ()
protected _default_where_clause ()
protected void _delete_tagvalue ()
protected _fetch_sequence_by_id ()
protected _final_clause ()
protected Listref _generic_fetch ()
protected _get_canonical_Member ()
protected _get_starting_lr_index ()
protected _left_join ()
protected _list_dbIDs ()
protected void _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 _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 delete_flattened_leaf ()
public delete_node ()
public delete_nodes_not_in_tree ()
public DESTROY ()
public dump_data ()
public
Bio::EnsEMBL::Compara::GeneTreeMember 
fetch_AlignedMember_by_member_id_mlssID ()
public
Bio::EnsEMBL::Compara::GeneTreeMember 
fetch_AlignedMember_by_member_id_root_id ()
public Arrayref fetch_all ()
public fetch_all_AlignedMembers_by_root_id ()
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 fetch_by_gene_Member_root_id ()
public
Bio::EnsEMBL::Compara::GeneTreeNode 
fetch_by_Member_root_id ()
public
Bio::EnsEMBL::Compara::GeneTreeNode 
fetch_by_stable_id ()
public
Bio::EnsEMBL::Compara::NestedSet 
fetch_first_shared_ancestor_indexed ()
public fetch_node_by_node_id ()
public 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 gene_member_id_is_in_tree ()
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 merge_nodes ()
public new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public store ()
public store_node ()
public store_tree ()
public void sync_tags_to_database ()
public Nothing sync_tree_leftright_index ()
public tables ()
public update ()
public update_node ()
public update_subtree ()

Method Documentation

protected Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::_add_GeneTree_wrapper ( ) [inherited]

Undocumented method

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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 Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::_fetch_sequence_by_id ( ) [inherited]

Undocumented method

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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::NCTreeAdaptor::_get_canonical_Member ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::_get_starting_lr_index ( ) [inherited]

Undocumented method

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

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

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::_objs_from_sth ( ) [inherited]

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 Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::_tag_capabilities ( ) [inherited]

Undocumented method

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

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::GeneTreeAdaptor::columns ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::create_instance_from_rowhash ( ) [inherited]

Undocumented method

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

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

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::delete_flattened_leaf ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::delete_node ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::delete_nodes_not_in_tree ( ) [inherited]

Undocumented method

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

Undocumented method

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public Bio::EnsEMBL::Compara::GeneTreeMember Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::fetch_AlignedMember_by_member_id_mlssID ( ) [inherited]
  Arg[1]     : int member_id of a peptide member (longest translation)
  Arg[2]     : [optional] int clusterset_id (def. 0)
  Example    :
      my $aligned_member = $proteintree_adaptor->
                            fetch_AlignedMember_by_member_id_mlssID
                            (
                             $member->get_canonical_peptide_Member->member_id, $mlssID
                            );
  Description: Fetches from the database the protein_tree that contains the member_id
  Returntype : Bio::EnsEMBL::Compara::GeneTreeMember
  Exceptions :
  Caller     :
 
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public Bio::EnsEMBL::Compara::GeneTreeMember Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::fetch_AlignedMember_by_member_id_root_id ( ) [inherited]
  Arg[1]     : int member_id of a peptide member (longest translation)
  Arg[2]     : [optional] int clusterset_id (def. 0)
  Example    :
      my $aligned_member = $proteintree_adaptor->
                            fetch_AlignedMember_by_member_id_root_id
                            (
                             $member->get_canonical_peptide_Member->member_id
                            );
  Description: Fetches from the database the protein_tree that contains the member_id
  Returntype : Bio::EnsEMBL::Compara::GeneTreeMember
  Exceptions :
  Caller     :
 
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public Arrayref Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::fetch_all ( ) [inherited]
  Arg[1]     : [optional] int clusterset_id (def. 1)
  Example    : $all_trees = $proteintree_adaptor->fetch_all(1);
  Description: Fetches from the database all the protein trees
  Returntype : arrayref of Bio::EnsEMBL::Compara::GeneTreeNode
  Exceptions :
  Caller     :
 
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::fetch_all_AlignedMembers_by_root_id ( ) [inherited]

Undocumented method

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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::GeneTreeAdaptor::fetch_all_roots ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::fetch_by_gene_Member_root_id ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::GeneTreeNode Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::fetch_by_Member_root_id ( ) [inherited]
  Arg[1]     : Bio::EnsEMBL::Compara::Member
  Arg[2]     : [optional] int clusterset_id (def. 1)
  Example    : $protein_tree = $proteintree_adaptor->fetch_by_Member_root_id($member);
  Description: Fetches from the database the protein_tree that contains the
               member. If you give it a clusterset id of 0 this will cause
               the search span across all known clustersets.
  Returntype : Bio::EnsEMBL::Compara::GeneTreeNode
  Exceptions :
  Caller     :
 
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public Bio::EnsEMBL::Compara::GeneTreeNode Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::fetch_by_stable_id ( ) [inherited]
  Arg[1]     : string $protein_tree_stable_id
  Example    : $protein_tree = $proteintree_adaptor->fetch_by_stable_id("ENSGT00590000083078");
  Description: Fetches from the database the protein_tree for that stable ID
  Returntype : Bio::EnsEMBL::Compara::GeneTreeNode
  Exceptions : returns undef if $stable_id is not found.
  Caller     :
 
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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::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::DBSQL::NestedSetAdaptor::fetch_parent_for_node ( ) [inherited]

Undocumented method

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

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::GeneTreeAdaptor::gene_member_id_is_in_tree ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::init_instance_from_rowhash ( ) [inherited]

Undocumented method

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

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

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::merge_nodes ( ) [inherited]

Undocumented method

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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::GeneTreeAdaptor::store ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::store_node ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::store_tree ( ) [inherited]

Undocumented method

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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
 
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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::GeneTreeAdaptor::tables ( ) [inherited]

Undocumented method

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

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

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor::update_node ( ) [inherited]

Undocumented method

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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: