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Bio::EnsEMBL::Compara::BaseRelation Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::BaseRelation:

List of all members.


Class Summary

Description

A superclass for pairwise and multiple relationships
Currently the AlignedMember objects are used in the GeneTree structure
to represent the leaves of the trees. Each leaf contains an aligned
sequence, which is represented as an AlignedMember object.
 

Definition at line 15 of file BaseRelation.pm.

Available Methods

protected Array _get_Member_Attribute ()
public
Bio::EnsEMBL::Compara::BaseRelationAdaptor 
adaptor ()
public void add_Member_Attribute ()
public Int dbID ()
public String description ()
public Array get_all_Member_Attribute ()
public Array get_all_Members ()
public Array get_Member_Attribute_by_GenomeDB ()
public Array get_Member_Attribute_by_source ()
public Array get_Member_Attribute_by_source_GenomeDB ()
public Array get_Member_Attribute_by_source_taxon ()
public Int Member_count_by_GenomeDB ()
public Int Member_count_by_source ()
public Int Member_count_by_source_GenomeDB ()
public Int Member_count_by_source_taxon ()
public Int method_link_id ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
method_link_species_set ()
public Int method_link_species_set_id ()
public String method_link_type ()
public
Bio::EnsEMBL::Compara::BaseRelation 
new ()
public new_fast ()
public String stable_id ()
public Int version ()

Method Documentation

protected Array Bio::EnsEMBL::Compara::BaseRelation::_get_Member_Attribute ( )
  Arg [1]    : string $attribute_scope
  Arg [2]    : string $key
  Example    : $domain->_get_Member_Attribute('_members_by_source', 'ENSEMBLPEP')
  Description: Used as the generic reference point for all 
               get_Memeber_Attribute_by* methods. The method searches the given
               scope & if the values cannot be found will initalize that value
               to an empty array reference.
  Returntype : array reference of Bio::EnsEMBL::Compara::Member
  Exceptions : None.
  Caller     : internal
 
Code:
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public Bio::EnsEMBL::Compara::BaseRelationAdaptor Bio::EnsEMBL::Compara::BaseRelation::adaptor ( )
  Arg [1]    : string $adaptor (optional)
               corresponding to a perl module
  Example    : 
  Description: getter/setter method for the adaptor for this relation. Usually
               this will be an object from a subclass of
               Bio::EnsEMBL::Compara::BaseRelationAdaptor
  Returntype : Bio::EnsEMBL::Compara::BaseRelationAdaptor object
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public void Bio::EnsEMBL::Compara::BaseRelation::add_Member_Attribute ( )
  Arg [1]    : arrayref of (Member, Attribute) objects
  Example    : 
  Description: Add a new pair of Member, Attribute objects to this relation
  Returntype : none
  Exceptions : Throws if input objects don't check
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseRelation::dbID ( )
  Arg [1]    : int $dbID (optional)
  Example    : 
  Description: Getter/setter for the internal ID of this relation
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::Compara::BaseRelation::description ( )
  Arg [1]    : string $description (optional)
  Example    : 
  Description: Getter/setter for the description corresponding to this relation
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Array Bio::EnsEMBL::Compara::BaseRelation::get_all_Member_Attribute ( )
  Arg [1]    : None
  Example    : 
  Description: 
  Returntype : array reference of [Bio::EnsEMBL::Compara::Member, Bio::EnsEMBL::Compara::Attribute]
  Exceptions : 
  Caller     :
 
Code:
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public Array Bio::EnsEMBL::Compara::BaseRelation::get_all_Members ( )
  Arg [1]    : None
  Example    : 
  Description: 
  Returntype : array reference of Bio::EnsEMBL::Compara::Member
  Exceptions : 
  Caller     : public
 
Code:
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public Array Bio::EnsEMBL::Compara::BaseRelation::get_Member_Attribute_by_GenomeDB ( )
  Arg [1]    : Bio::EnsEMBL::Compara::GenomeDB $genome_db
  Example    : $domain->get_Member_Attribute_by_GenomeDB($genome_db)
  Description: Returns all [Member_Attribute] entries linked to this GenomeDB. 
               This will only return EnsEMBL based entries since UniProtKB 
               entries are not linked to a GenomeDB.
  Returntype : array reference of Bio::EnsEMBL::Compara::Member
  Exceptions : If input is undefined & genome db is not of expected type
  Caller     : public
 
Code:
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public Array Bio::EnsEMBL::Compara::BaseRelation::get_Member_Attribute_by_source ( )
  Arg [1]    : string $source_name
               e.g. "ENSEMBLPEP"
  Example    : 
  Description: 
  Returntype : array reference of Bio::EnsEMBL::Compara::Member and attribute
  Exceptions : 
  Caller     : public
 
Code:
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public Array Bio::EnsEMBL::Compara::BaseRelation::get_Member_Attribute_by_source_GenomeDB ( )
  Arg [1]    : string $source_name
  Arg [2]    : Bio::EnsEMBL::Compara::GenomeDB $genome_db
  Example    : $domain->get_Member_by_source_taxon('ENSEMBLPEP', $genome_db)
  Description: Returns all [Member_Attribute] entries linked to this GenomeDB
               and the given source_name. This will only return EnsEMBL based 
               entries since UniProtKB entries are not linked to a GenomeDB.
  Returntype : array reference of Bio::EnsEMBL::Compara::Member
  Exceptions : If input is undefined & genome db is not of expected type
  Caller     : public
 
Code:
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public Array Bio::EnsEMBL::Compara::BaseRelation::get_Member_Attribute_by_source_taxon ( )
  Arg [1]    : string $source_name
  Arg [2]    : int $taxon_id
  Example    : $domain->get_Member_by_source_taxon('ENSEMBLPEP',9606)
  Description: 
  Returntype : array reference of Bio::EnsEMBL::Compara::Member
  Exceptions : 
  Caller     : public
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseRelation::Member_count_by_GenomeDB ( )
  Arg [1]    : Bio::EnsEMBL::Compara::GenomeDB $genome_db
  Example    : Member_count_by_GenomeDB($genome_db);
  Description: Convenience wrapper for member counts by a GenomeDB
  Returntype : int
  Exceptions : Thrown by subrountines this call. See get_Member_Attribute 
               equivalent
  Caller     : public
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseRelation::Member_count_by_source ( )
  Arg [1]    : string $source_name
               e.g. "ENSEMBLPEP"
  Example    : $domain->Member_count_by_source('ENSEMBLPEP');
  Description: 
  Returntype : int
  Exceptions : 
  Caller     : public
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseRelation::Member_count_by_source_GenomeDB ( )
  Arg [1]    : string $source_name
  Arg [2]    : Bio::EnsEMBL::Compara::GenomeDB $genome_db
  Example    : Member_count_by_source_GenomeDB('ENSEMBLPEP', $genome_db);
  Description: Convenience wrapper for member counts by a GenomeDB
  Returntype : int
  Exceptions : Thrown by subrountines this call. See get_Member_Attribute 
               equivalent
  Caller     : public
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseRelation::Member_count_by_source_taxon ( )
  Arg [1]    : string $source_name
  Arg [2]    : int $taxon_id
  Example    : Member_count_by_source_taxon('ENSEMBLPEP',9606);
  Description: 
  Returntype : int
  Exceptions : 
  Caller     : public
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseRelation::method_link_id ( )
  Arg [1]    : integer (optional)
  Example    : 
  Description: getter/setter method for the method_link_id for this relation.
               Can obtain the data from the method_link_species_set object.
  Returntype : integer
  Exceptions : Throws when getting if both this value and the method_link_species_set
               are unset.
  Caller     : general
  Status     : Stable
 
public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::BaseRelation::method_link_species_set ( )
  Arg [1]    : MethodLinkSpeciesSet object (optional)
  Example    : 
  Description: getter/setter method for the MethodLinkSpeciesSet for this relation.
               Can lazy-load the method_link_species_set from the method_link_species_set_id
               if that one is set and the adaptor is set.
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
  Exceptions : throws if setting to an unsuitable object 
  Caller     : general
  Status     : Stable
 
public Int Bio::EnsEMBL::Compara::BaseRelation::method_link_species_set_id ( )
  Arg [1]    : integer (optional)
  Example    : 
  Description: getter/setter method for the internal ID of the MethodLinkSpeciesSet
               for this relation.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
public String Bio::EnsEMBL::Compara::BaseRelation::method_link_type ( )
  Arg [1]    : string $method_link_type (optional)
  Example    : 
  Description: getter/setter method for the method_link_type for this relation.
               Can obtain the data from the method_link_species_set object.
  Returntype : string
  Exceptions : Throws when getting if both this value and the method_link_species_set
               are unset.
  Caller     : general
  Status     : Stable
 
public Bio::EnsEMBL::Compara::BaseRelation Bio::EnsEMBL::Compara::BaseRelation::new ( )
  Arg [-DBID]  : 
       int - internal ID for this object
  Arg [-ADAPTOR]:
        Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor - the object adaptor
  Arg [-STABLE_ID] :
        string - the stable identifier of this object
  Arg [-VERSION] :
        int - the version of the stable identifier of this object
  Arg [-METHOD_LINK_SPECIES_SET_ID] :
        int - the internal ID for the MethodLinkSpeciesSet object
  Arg [-METHOD_LINK_TYPE] :
        string - the method_link_type
  Arg [-DESCRIPTION]:
        string - the description for the object
  Example    : $family = Bio::EnsEMBL::Compara::BaseRelation->new(...);
  Description: Creates a new BaseRelation object
  Returntype : Bio::EnsEMBL::Compara::BaseRelation
  Exceptions : none
  Caller     : subclass->new
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::Family.

public Bio::EnsEMBL::Compara::BaseRelation::new_fast ( )
  Arg [1]    : hash reference $hashref
  Example    : none
  Description: This is an ultra fast constructor which requires knowledge of
               the objects internals to be used.
  Returntype : 
  Exceptions : none
  Caller     : 
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::Compara::BaseRelation::stable_id ( )
  Arg [1]    : string $stable_id (optional)
  Example    : 
  Description: Getter/setter for the stable ID of this relation
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseRelation::version ( )
  Arg [1]    : string $version (optional)
  Example    : 
  Description: Getter/setter for the version number of the stable ID
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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The documentation for this class was generated from the following file: