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

List of all members.


Class Summary

Definition at line 10 of file Family.pm.

Available Methods

protected Array _get_Member_Attribute ()
protected Array _run_finder_by_member_field_source_name ()
public
Bio::EnsEMBL::Compara::BaseRelationAdaptor 
adaptor ()
public void add_Member_Attribute ()
public Int dbID ()
public String description ()
public description_score ()
public Array get_all_GenomeDBs_by_member_source_name ()
public Array get_all_Member_Attribute ()
public Array get_all_Members ()
public Array get_all_taxa_by_member_source_name ()
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 get_SimpleAlign ()
public load_cigars_from_fasta ()
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::Family 
new ()
public new_fast ()
public void read_clustalw ()
public String stable_id ()
public Int version ()

Method Documentation

protected Array Bio::EnsEMBL::Compara::BaseRelation::_get_Member_Attribute ( ) [inherited]
  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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protected Array Bio::EnsEMBL::Compara::Family::_run_finder_by_member_field_source_name ( )
  Arg [1]    : string $entity
               e.g. 'taxa' or 'genome_db'
  Arg [2]    : string $source_name (not required)
               e.g. 'ENSEMBLPEP'
  Arg [3]    : code $sub
               e.g. 'taxa' or 'genome_db'          
  Example    : 
  Description: 
  Returntype : array reference of distinct objects as returned by your 
               subroutine 
  Exceptions : If an unknown entity has been given
  Caller     : private
 
Code:
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public Bio::EnsEMBL::Compara::BaseRelationAdaptor Bio::EnsEMBL::Compara::BaseRelation::adaptor ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 Bio::EnsEMBL::Compara::Family::description_score ( )
  Arg [1]    : 
  Example    : 
  Description: 
  Returntype : 
  Exceptions : 
  Caller     :
 
Code:
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public Array Bio::EnsEMBL::Compara::Family::get_all_GenomeDBs_by_member_source_name ( )
  Arg [1]    : string $source_name
               e.g. "ENSEMBLPEP"
  Example    : 
  Description: Returns the distinct GenomeDBs found in this family. Please note
               that if you specify a source other than an EnsEMBL based one
               the chances of getting back GenomeDBs are very low.
  Returntype : array reference of distinct Bio::EnsEMBL::Compara::GenomeDB 
               objects found in this family
  Exceptions : 
  Caller     : public
 
Code:
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public Array Bio::EnsEMBL::Compara::BaseRelation::get_all_Member_Attribute ( ) [inherited]
  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 ( ) [inherited]
  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::Family::get_all_taxa_by_member_source_name ( )
  Arg [1]    : string $source_name
               e.g. "ENSEMBLPEP"
  Example    : 
  Description: Returns the distinct taxons found in this family across
               the specified source. If you do not specify a source then
               the code will return all taxons in this family.
  Returntype : array reference of distinct Bio::EnsEMBL::Compara::NCBITaxon 
               objects found in this family
  Exceptions : 
  Caller     : public
 
Code:
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public Array Bio::EnsEMBL::Compara::BaseRelation::get_Member_Attribute_by_GenomeDB ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 Bio::EnsEMBL::Compara::Family::get_SimpleAlign ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Family::load_cigars_from_fasta ( )

Undocumented method

Code:
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public Int Bio::EnsEMBL::Compara::BaseRelation::Member_count_by_GenomeDB ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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 ( ) [inherited]
  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::Family Bio::EnsEMBL::Compara::Family::new ( )
  Arg [1]    : 
  Example    : 
  Description: 
  Returntype : Bio::EnsEMBL::Compara::Family (but without members; caller has to fill using
               add_member)
  Exceptions : 
  Caller     :
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::BaseRelation.

public Bio::EnsEMBL::Compara::BaseRelation::new_fast ( ) [inherited]
  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 void Bio::EnsEMBL::Compara::Family::read_clustalw ( )
  Arg [1]    : string $file 
               The name of the file containing the clustalw output  
  Example    : $family->read_clustalw('/tmp/clustalw.aln');
  Description: Parses the output from clustalw and sets the alignment strings
               of each of the memebers of this family
  Returntype : none
  Exceptions : thrown if file cannot be parsed
               warning if alignment file contains identifiers for sequences
               which are not members of this family
  Caller     : general
 
Code:
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public String Bio::EnsEMBL::Compara::BaseRelation::stable_id ( ) [inherited]
  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 ( ) [inherited]
  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: