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Bio::EnsEMBL::Variation::VariationSet Class Reference
Inheritance diagram for Bio::EnsEMBL::Variation::VariationSet:

List of all members.


Class Summary

Synopsis

Description

This is a class representing a set of variations that are grouped by e.g.
study, method, quality measure etc.
 

Definition at line 24 of file VariationSet.pm.

Available Methods

protected _get_bitvalue ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public Int dbID ()
public String description ()
public get_all_DAS_Features ()
public Reference get_all_StructuralVariations ()
public Reference get_all_sub_VariationSets ()
public Reference get_all_super_VariationSets ()
public Reference get_all_VariationFeatures_by_Slice ()
public Reference get_all_Variations ()
public
Bio::EnsEMBL::Utils::Iterator 
get_StructuralVariation_Iterator ()
public
Bio::EnsEMBL::Utils::Iterator 
get_Variation_Iterator ()
public Boolean is_stored ()
public String name ()
public
Bio::EnsEMBL::Variation::VariationSet 
new ()
public String short_name ()

Method Documentation

protected Bio::EnsEMBL::Variation::VariationSet::_get_bitvalue ( )

Undocumented method

Code:
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public String Bio::EnsEMBL::Variation::VariationSet::description ( )
  Arg [1]    : string $description
  Example    : print $vs->description();
  Description: Getter/Setter for the description of this VariationSet
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Reference Bio::EnsEMBL::Variation::VariationSet::get_all_StructuralVariations ( )
  Example    : print $vs->get_all_StructuralVariations();
  Description: Gets all structural variations belonging to this variation set and all of its subsets.
  Returntype : reference to list of Bio::EnsEMBL::Variation::StructuralVariation
  Exceptions : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Reference Bio::EnsEMBL::Variation::VariationSet::get_all_sub_VariationSets ( )
  Arg [1]    : (optional) boolean $only_immediate
               If true, will only get the direct subsets of this variation. The default behaviour is
               to recursively get all subsets.
  Example    : print $vs->get_all_sub_VariationSets();
  Description: Recursively gets all variation sets that are subsets of this variation set.
  Returntype : reference to list of Bio::EnsEMBL::Variation::VariationSet
  Exceptions : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Reference Bio::EnsEMBL::Variation::VariationSet::get_all_super_VariationSets ( )
  Arg [1]    : (optional) boolean $only_immediate
               If true, will only get the direct supersets of this variation. The default behaviour is
               to recursively get all supersets.
  Example    : print $vs->get_all_super_VariationSets();
  Description: Recursively gets all variation sets that are above this variation set.
  Returntype : reference to list of Bio::EnsEMBL::Variation::VariationSet
  Exceptions : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Reference Bio::EnsEMBL::Variation::VariationSet::get_all_VariationFeatures_by_Slice ( )
  Arg [1]    : Bio::EnsEMBL:Variation::Slice $slice
  Example    : my @vfs =
@{$vs->get_all_VariationFeatures_by_Slice($slice)};
  Description: Retrieves all variation features in a slice that belong to 
			   this set.
  Returntype : reference to list Bio::EnsEMBL::Variation::VariationFeature
  Exceptions : throw on bad argument
  Caller     : general
  Status     : Stable
 
Code:
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public Reference Bio::EnsEMBL::Variation::VariationSet::get_all_Variations ( )
  Example    : print $vs->get_all_Variations();
  Description: Gets all variations belonging to this variation set and all of its subsets.
  Returntype : reference to list of Bio::EnsEMBL::Variation::Variation
  Exceptions : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::Variation::VariationSet::get_StructuralVariation_Iterator ( )
  Example    : my $sv_iterator = $vs->get_StructuralVariation_Iterator;
  Description: Gets an iterator over all structural variations belonging to this 
	             variation set and all of its subsets.
  Returntype : Bio::EnsEMBL::Utils::Iterator
  Exceptions : none
  Caller     : general
  Status     : Experimental
 
Code:
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public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::Variation::VariationSet::get_Variation_Iterator ( )
  Example    : my $var_iterator = $vs->get_Variation_Iterator;
  Description: Gets an iterator over  all variations belonging to this 
	             variation set and all of its subsets.
  Returntype : Bio::EnsEMBL::Utils::Iterator
  Exceptions : none
  Caller     : general
  Status     : Experimental
 
Code:
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public String Bio::EnsEMBL::Variation::VariationSet::name ( )
  Arg [1]    : string $name
  Example    : print $vs->name();
  Description: Getter/Setter for the name of this VariationSet
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Bio::EnsEMBL::Variation::VariationSet Bio::EnsEMBL::Variation::VariationSet::new ( )
  Arg [dbID] :
    int - unique internal identifier for this allele group
  Arg [ADAPTOR] :
    Bio::EnsEMBL::Variation::DBSQL::VariationSetAdaptor
  Arg [NAME] :
    string - the name of this variation set
  Arg [DESCRIPTION] :
    string - A description explaining the charcteristics of this variation set
  Arg [SHORT_NAME] :
    string - the short name of this variation set
  Example    :
    $ag = Bio::EnsEMBL::Variation::VariationSet->new
      (
       -dbID => 12,
       -adaptor => $var_set_adaptor,
       -name   => 'Phenotype-associated variations',
       -description => 'Variations that have been associated with a phenotype',
       -short_name => 'ph_variants'
      );
  Description: Constructor.  Instantiates a new VariationSet
  Returntype : Bio::EnsEMBL::Variation::VariationSet
  Exceptions : none
  Caller     : general
  Status     : At Risk
 
Code:
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Reimplemented from Bio::EnsEMBL::Storable.

public String Bio::EnsEMBL::Variation::VariationSet::short_name ( )
  Arg [1]    : string $short_name
  Example    : print $vs->short_name();
  Description: Getter/Setter for the short name of this VariationSet
  Returntype : string
  Exceptions : none
  Caller     : general
 
Code:
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The documentation for this class was generated from the following file: