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

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Registry;

  my $homology_adaptor = $reg-\>get_adaptor("Multi", "compara", "Homology");

  ## Please, refer to Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor
  ## to see how to get a Member from the database. Also, you can
  ## find alternative ways to fetch homologies in the POD for the
  ## Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor module.

  my $homologies = $homology_adaptor-\>fetch_all_by_Member($member);

  foreach my $this_homology (@$homologies) {
    my $homologue_genes = $this_homology-\>gene_list();
    print join(" and ", @$homologue_genes), " are ",
        $this_homology-\>description, "\n";
  }

Definition at line 28 of file Homology.pm.

Available Methods

protected Array _get_Member_Attribute ()
public
Bio::EnsEMBL::Compara::BaseRelationAdaptor 
adaptor ()
public void add_Member_Attribute ()
public Int ancestor_node_id ()
public Int dbID ()
public String description ()
public Floating dn ()
public Floating dnds_ratio ()
public Floating ds ()
public FourD_codon ()
public Array gene_list ()
public Bio::SimpleAlign get_4D_SimpleAlign ()
public Array get_all_Member_Attribute ()
public Array get_all_Members ()
public Array get_all_PeptideAlignFeature ()
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 Bio::SimpleAlign get_SimpleAlign ()
public Boolean has_species_by_name ()
public String homology_key ()
public Float lnl ()
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 Float n ()
public
Bio::EnsEMBL::Compara::BaseRelation 
new ()
public new_fast ()
public Int node_id ()
public print_homology ()
public Float s ()
public String stable_id ()
public String subtype ()
public String taxonomy_alias ()
public String taxonomy_level ()
public Float threshold_on_ds ()
public Int tree_node_id ()
public TwoD_codon ()
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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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::Homology::ancestor_node_id ( )
  Arg [1]    : int $ancestor_node_id (optional)
  Example    : $ancestor_node_id = $homology->ancestor_node_id();
               $homology->subtype($ancestor_node_id);
  Description: getter/setter of integer that refer to the ancestor_node_id in the protein_tree data.
  Returntype : int
  Exceptions : none
  Caller     : general
 
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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
 
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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 Floating Bio::EnsEMBL::Compara::Homology::dn ( )
  Arg [1]    : floating $dn (can be undef)
  Arg [2]    : boolean $apply_threshold_on_ds (optional, default = 1)
               Can be 0 or 1.
  Example    : $homology->dn or $homology->dn(0.1209)
               if you want to retrieve dn without applying threshold_on_ds, the right call
               is $homology->dn(undef,0).
  Description: set/get the non synonymous subtitution rate
  Returntype : floating
  Exceptions : 
  Caller     :
 
Code:
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public Floating Bio::EnsEMBL::Compara::Homology::dnds_ratio ( )
  Arg [1]    : boolean $apply_threshold_on_ds (optional, default = 1)
               Can be 0 or 1. 
  Example    : $homology->dnds_ratio or
               $homology->dnds_ratio(0) if you want to obtain a result
               even when the dS is above the threshold on dS.
  Description: return the ratio of dN/dS
  Returntype : floating
  Exceptions : 
  Caller     :
 
Code:
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public Floating Bio::EnsEMBL::Compara::Homology::ds ( )
  Arg [1]    : floating $ds (can be undef)
  Arg [2]    : boolean $apply_threshold_on_ds (optional, default = 1)
               Can be 0 or 1. 
  Example    : $homology->ds or $homology->ds(0.9846)
               if you want to retrieve ds without applying threshold_on_ds, the right call
               is $homology->dn(undef,0).
  Description: set/get the synonymous subtitution rate
  Returntype : floating
  Exceptions : 
  Caller     :
 
Code:
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public Bio::EnsEMBL::Compara::Homology::FourD_codon ( )

Undocumented method

Code:
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public Array Bio::EnsEMBL::Compara::Homology::gene_list ( )
  Example    : my $pair = $homology->gene_list
  Description: return the pair of members for the homology
  Returntype : array ref of (2) Bio::EnsEMBL::Compara::Member objects
  Caller     : general
 
Code:
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public Bio::SimpleAlign Bio::EnsEMBL::Compara::Homology::get_4D_SimpleAlign ( )
  Example    : $4d_align = $homology->get_4D_SimpleAlign();
  Description: get 4 times degenerate positions pairwise simple alignment
  Returntype : Bio::SimpleAlign
 
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     :
 
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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::Homology::get_all_PeptideAlignFeature ( )
  Example    : my ($paf) = @{$homology->get_all_PeptideAlignFeature};
               my ($paf, $recipPaf) = @{$homology->get_all_PeptideAlignFeature};
  Description: return the peptide_align_feature object (and its reciprocal hit)
               used to create this homology
  Returntype : array ref of peptide_align_feature objects
  Exceptions :
  Caller     :
 
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::SimpleAlign Bio::EnsEMBL::Compara::Homology::get_SimpleAlign ( )
  Arg [1]    : string 'cdna' (optional)
  Example    : $simple_align = $homology->get_SimpleAlign();
               $cdna_s_align = $homology->get_SimpleAlign('cdna');
  Description: get pairwise simple alignment (from the multialignment)
  Returntype : Bio::SimpleAlign
 
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public Boolean Bio::EnsEMBL::Compara::Homology::has_species_by_name ( )
  Arg [1]    : string $species_name
  Example    : my $ret = $homology->has_species_by_name("Homo sapiens");
  Description: return TRUE or FALSE whether one of the members in the homology is from the given species
  Returntype : 1 or 0
  Exceptions :
  Caller     :
 
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public String Bio::EnsEMBL::Compara::Homology::homology_key ( )
  Example    : my $key = $homology->homology_key;
  Description: returns a string uniquely identifying this homology in world space.
               uses the gene_stable_ids of the members and orders them by taxon_id
               and concatonates them together.  
  Returntype : string
  Exceptions :
  Caller     :
 
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public Float Bio::EnsEMBL::Compara::Homology::lnl ( )
  Arg [1]    : float $lnl (optional)
  Example    : $lnl = $homology->lnl();
               $homology->lnl(-1234.567);
  Description: getter/setter of number of the negative log likelihood for the dnds homology calculation.
  Returntype : float
  Exceptions : none
  Caller     : general
 
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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
 
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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
 
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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
 
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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
 
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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 Float Bio::EnsEMBL::Compara::Homology::n ( )
  Arg [1]    : float $n (optional)
  Example    : $n = $homology->n();
               $homology->n(3);
  Description: getter/setter of number of nonsynonymous positions for the homology.
  Returntype : float
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::BaseRelation Bio::EnsEMBL::Compara::BaseRelation::new ( ) [inherited]
  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 ( ) [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
 
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public Int Bio::EnsEMBL::Compara::Homology::node_id ( )
  Arg [1]    : int $node_id (optional)
  Example    : $node_id = $homology->node_id();
               $homology->subtype($node_id);
  Description: getter/setter of integer that refer to a node_id in the protein_tree data.
  Returntype : int
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Homology::print_homology ( )
 Example    : $homology->print_homology
 Description: This method prints a short descriptor of the homology
	      USE ONLY FOR DEBUGGING not for data output since the
	      format of this output may change as need dictates.
 
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public Float Bio::EnsEMBL::Compara::Homology::s ( )
  Arg [1]    : float $s (optional)
  Example    : $s = $homology->s();
               $homology->s(4);
  Description: getter/setter of number of synonymous positions for the homology.
  Returntype : float
  Exceptions : none
  Caller     : general
 
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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
 
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public String Bio::EnsEMBL::Compara::Homology::subtype ( )
  Arg [1]    : string $subtype (optional)
  Example    : $subtype = $homology->subtype();
               $homology->subtype($subtype);
  Description: getter/setter of string description of homology subtype.
               Examples: 'Chordata', 'Euteleostomi', 'Homo sapiens'
  Returntype : string
  Exceptions : none
  Caller     : general
 
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public String Bio::EnsEMBL::Compara::Homology::taxonomy_alias ( )
  Arg [1]    : string $taxonomy_alias (optional)
  Example    : $taxonomy_alias = $homology->taxonomy_alias();
               $homology->taxonomy_alias($taxonomy_alias);
  Description: get string description of homology taxonomy_alias.
               Examples: 'Chordates', 'Bony vertebrates', 'Homo sapiens'
               Defaults to taxonomy_level if alias is not in the db
  Returntype : string
  Exceptions : none
  Caller     : general
 
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public String Bio::EnsEMBL::Compara::Homology::taxonomy_level ( )
  Arg [1]    : string $taxonomy_level (optional)
  Example    : $taxonomy_level = $homology->taxonomy_level();
               $homology->taxonomy_level($taxonomy_level);
  Description: getter/setter of string description of homology taxonomy_level.
               Examples: 'Chordata', 'Euteleostomi', 'Homo sapiens'
  Returntype : string
  Exceptions : none
  Caller     : general
 
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public Float Bio::EnsEMBL::Compara::Homology::threshold_on_ds ( )
  Arg [1]    : float $threshold_ond_ds (optional)
  Example    : $lnl = $homology->threshold_on_ds();
               $homology->threshold_on_ds(1.01340);
  Description: getter/setter of the threshold on ds for which the dnds ratio still makes sense.
  Returntype : float
  Exceptions : none
  Caller     : general
 
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public Int Bio::EnsEMBL::Compara::Homology::tree_node_id ( )
  Arg [1]    : int $tree_node_id (optional)
  Example    : $tree_node_id = $homology->tree_node_id();
               $homology->subtype($tree_node_id);
  Description: getter/setter of integer that refer to the tree node_id in the protein_tree data.
  Returntype : int
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Homology::TwoD_codon ( )

Undocumented method

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