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

List of all members.


Class Summary

Definition at line 8 of file HomologyAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected String _final_clause ()
protected A _join ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _recursive_get_orthocluster ()
protected _straight_join ()
protected _tables ()
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 An fetch_all_by_genome_pair ()
public An fetch_all_by_Member ()
public An fetch_all_by_Member_method_link_type ()
public An fetch_all_by_Member_MethodLinkSpeciesSet ()
public An fetch_all_by_Member_paired_species ()
public fetch_all_by_method_link_type ()
public An fetch_all_by_MethodLinkSpeciesSet ()
public An fetch_all_by_MethodLinkSpeciesSet_orthology_type ()
public An fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype ()
public An fetch_all_by_tree_node_id ()
public An fetch_all_orphans_by_GenomeDB ()
public Bio::EnsEMBL::SeqFeature fetch_by_dbID ()
public A fetch_by_Member_id_Member_id ()
public An fetch_by_Member_Member_method_link_type ()
public A fetch_by_PMember_id_PMember_id ()
public Bio::EnsEMBL::SeqFeature fetch_by_stable_id ()
public An fetch_orthocluster_with_Member ()
public Arrayref generic_fetch ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public Int store ()
public store_relation ()
public update_genetic_distance ()
public update_relation ()

Method Documentation

protected Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::_columns ( )

Undocumented method

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

protected Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::_default_where_clause ( )

Undocumented method

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

protected String Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::_final_clause ( ) [inherited]
  Arg [1]    : none
  Example    : none
  Description: May be overriden to provide an additional clause to the end
               of the SQL query used to fetch feature records.
               This is useful to add a required ORDER BY clause to the
               query for example.
  Returntype : string
  Exceptions : none
  Caller     : generic_fetch
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected A Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::_join ( ) [inherited]
  Arg [1]    : none
  Example    : none
  Description: Can be overridden by a subclass to specify any left joins
               which should occur. The table name specigfied in the join
               must still be present in the return values of
  Returntype : a {'tablename' => 'join condition'} pair
  Exceptions : none
  Caller     : general
 
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protected Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::_objs_from_sth ( )

Undocumented method

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

protected Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::_recursive_get_orthocluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::_tables ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::fetch_all ( ) [inherited]

Undocumented method

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

public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_genome_pair ( )
  Arg [1]    : genome_db_id
  Arg [2]    : genome_db_id
  Example    : $homologies = $HomologyAdaptor->fetch_all_by_genome_pair(22,3);
  Description: fetch all the homology relationships for the a pair of genome_db_ids
               This method can be used to grab all the orthologues for a species pair.
  Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
  Exceptions : none
  Caller     :
 
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public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_Member ( )
 Arg [1]    : Bio::EnsEMBL::Compara::Member $member
 Example    : $homologies = $HomologyAdaptor->fetch_all_by_Member($member);
 Description: fetch the homology relationships where the given member is implicated
 Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
 Exceptions : none
 Caller     : general
 
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public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_Member_method_link_type ( )
  Arg [1]    : Bio::EnsEMBL::Compara::Member $member
  Arg [2]    : string $method_link_type
  Example    : $homologies = $HomologyAdaptor->fetch_all_by_Member_method_link_type(
                   $member, "ENSEMBL_ORTHOLOGUES");
  Description: fetch the homology relationships where the given member is implicated
               in a relationship of the type defined by $method_link_type.
  Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
  Exceptions : none
  Caller     :
 
public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_Member_MethodLinkSpeciesSet ( )
  Arg [1]    : Bio::EnsEMBL::Compara::Member $member
  Arg [2]    : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
  Example    : $homologies = $HomologyAdaptor->fetch_all_by_Member_MethodLinkSpeciesSet($member, $mlsss);
  Description: fetch the homology relationships for a given $member and $mlss.
  Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
  Exceptions : none
  Caller     :
 
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public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_Member_paired_species ( )
  Arg [1]    : Bio::EnsEMBL::Compara::Member $member
  Arg [2]    : string $species
               e.g. "Mus_musculus" or "Mus musculus"
  Arg [3]    : (optional) an arrayref of method_link types
               e.g. ['ENSEMBL_ORTHOLOGUES']. Default is ['ENSEMBL_ORTHOLOGUES','ENSEMBL_PARALOGUES']
  Example    : $homologies = $HomologyAdaptor->fetch_all_by_Member_paired_species($member, "Mus_musculus");
  Description: fetch the homology relationships where the given member is implicated
               in pair with another member from the paired species. Member species and
               paired species should be different.
               When you give the species name the method attempts to find
               the species without _ subsitution and then replacing them
               for spaces. This is to help support GenomeDB objects which
               have _ in their names.
  Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
  Exceptions : If a GenomeDB cannot be found for the given species name
  Caller     :
 
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public Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::fetch_all_by_method_link_type ( ) [inherited]

Undocumented method

public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_MethodLinkSpeciesSet ( )
  Arg [1]    : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
  Example    : $homologies = $HomologyAdaptor->fetch_all_by_MethodLinkSpeciesSet($mlss);
  Description: fetch all the homology relationships for the given MethodLinkSpeciesSet
               Since each species pair Orthologue analysis is given a unique 
	       MethodLinkSpeciesSet, this method can be used to grab all the 
	       orthologues for a species pair.
  Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
  Exceptions : none
  Caller     :
 
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public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_MethodLinkSpeciesSet_orthology_type ( )
  Arg [1]    : method_link_species_set
  Arg [2]    : orthology type
  Example    : $homologies = $HomologyAdaptor->
                  fetch_all_by_MethodLinkSpeciesSet_orthology_type(
                  $mlss, 'ortholog_one2one');
  Description: fetch all the homology relationships for the given
               orthology type and for a mlss (corresponding to one or
               a pair of genomes). This method can be used to grab all
               the orthologues for one genome paralogues or a species
               pair and an orthology type.
  Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
  Exceptions : none
  Caller     :
 
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public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype ( )
  Arg [1]    : method_link_species_set
  Arg [2]    : orthology type
  Arg [3]    : orthology subtype
  Example    : $homologies = $HomologyAdaptor->
                  fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype(
                  $mlss, 'ortholog_one2one','Mammalia');
  Description: fetch all the homology relationships for the given
               orthology type, mlss (corresponding to one or
               a pair of genomes) and subtype (taxonomy level). This method can be
               used to grab all the orthologues for one genome paralogues or a species
               pair and an orthology type and taxonomy level.
  Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
  Exceptions : none
  Caller     :
 
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public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_tree_node_id ( )
  Arg [1]    : int $tree_node_id
  Example    : $homologies = $HomologyAdaptor->fetch_all_by_tree_node_id($tree->node_id);
  Description: fetch all the homology relationships for the given tree
  Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
  Exceptions : none
  Caller     :
 
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public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_orphans_by_GenomeDB ( )
 Arg [1]    : Bio::EnsEMBL::Compara::GenomeDB $genome_db
 Example    : $HomologyAdaptor->fetch_all_orphans_by_GenomeDB($genome_db);
 Description: fetch the members for a genome_db that have no homologs in the database
 Returntype : an array reference of Bio::EnsEMBL::Compara::Member objects
 Exceptions : when isa if Arg [1] is not Bio::EnsEMBL::Compara::GenomeDB
 Caller     : general
 
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public Bio::EnsEMBL::SeqFeature Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::fetch_by_dbID ( ) [inherited]
  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234);
  Description: Returns the feature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::SeqFeature
  Exceptions : thrown if $id is not defined
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public A Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_by_Member_id_Member_id ( )
  Arg [1]    : int $member_id1
  Arg [2]    : int $member_id2
  Example    : $homologies = $HomologyAdaptor->fetch_by_Member_id_Member_id(
                   $member_id1, $member_id2);
  Description: fetch the homology relationships for a given member_id pair
  Returntype : a Bio::EnsEMBL::Compara::Homology object
  Exceptions : none
  Caller     :
 
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public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_by_Member_Member_method_link_type ( )
  Arg [1]    : Bio::EnsEMBL::Compara::Member $member
  Arg [2]    : Bio::EnsEMBL::Compara::Member $member
  Arg [3]    : string $method_link_type
  Example    : $homologies = $HomologyAdaptor->fetch_by_Member_Member_method_link_type(
                   $member1->gene_member, $member2->gene_member, "ENSEMBL_ORTHOLOGUES");
  Description: fetch the homology relationships where the given member pair is implicated
               in a relationship of the type defined by $method_link_type.
  Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
  Exceptions : none
  Caller     :
 
public A Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_by_PMember_id_PMember_id ( )
  Arg [1]    : int $member_id1
  Arg [2]    : int $member_id2
  Example    : $homologies = $HomologyAdaptor->fetch_by_Member_id_Member_id(
                   $member_id1, $member_id2);
  Description: fetch the homology relationships for a given peptide_member_id pair
  Returntype : a Bio::EnsEMBL::Compara::Homology object
  Exceptions : none
  Caller     :
 
Code:
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public Bio::EnsEMBL::SeqFeature Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::fetch_by_stable_id ( ) [inherited]
  Arg [1]    : string $stable_id
               the unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234);
  Description: Returns the feature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::SeqFeature
  Exceptions : thrown if $stable_id is not defined
  Caller     : general
 
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public An Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_orthocluster_with_Member ( )
  Arg [1]    : Bio::EnsEMBL::Compara::Member $gene_member (must be ENSEMBLGENE type)
  Example    : my ($homology_list, $gene_list) = 
                 $HomologyAdaptor->fetch_orthocluster_with_Member($gene_member);
  Description: do a recursive search starting from $gene_member to find the cluster of
               all connected genes and homologies via connected components clustering.
  Returntype : an array pair of array references.  
               First array_ref is the list of Homology objects in the cluster graph
	       Second array ref is the list of unique gene Members in the cluster
  Exceptions : none
  Caller     :
 
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public Arrayref Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::generic_fetch ( ) [inherited]
  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
               e.g. "fm.family_id = $family_id"
  Arg [2]    : (optional) arrayref $join
               the arrayref $join should contain arrayrefs of this form
               [['family_member', 'fm'],
                # the table to join with synonym (mandatory) as an arrayref
                'm.member_id = fm.member_id',
                # the join condition (mandatory)
                [qw(fm.family_id fm.member_id fm.cigar_line)]]
                # any additional columns that the join could imply (optional)
                # as an arrayref 
  Example    : $arrayref = $a->generic_fetch($constraint, $join);
  Description: Performs a database fetch and returns BaseRelation-inherited objects
  Returntype : arrayref of Bio::EnsEMBL::Compara::BaseRelation-inherited objects
  Exceptions : none
  Caller     : various adaptors' specific fetch_ subroutines
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Int Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::store ( )
 Arg [1]    : Bio::EnsEMBL::Compara::Homology $homology
 Example    : $HomologyAdaptor->store($homology)
 Description: Stores a homology object into a compara database
 Returntype : int 
              been the database homology identifier, if homology stored correctly
 Exceptions : when isa if Arg [1] is not Bio::EnsEMBL::Compara::Homology
 Caller     : general
 
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public Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::store_relation ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::update_genetic_distance ( )
 Arg [1]    : Bio::EnsEMBL::Compara::Homology $homology
 Example    : $HomologyAdaptor->update_genetic_distance($homology)
 Description: updates the n,s,dn,ds,lnl values from a homology object into a compara database
 Exceptions : when isa if Arg [1] is not Bio::EnsEMBL::Compara::Homology
 Caller     : Bio::EnsEMBL::Compara::Runnable::Homology_dNdS
 
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public Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::update_relation ( ) [inherited]

Undocumented method

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