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Bio::EnsEMBL::Compara::AlignSlice::Translation Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::AlignSlice::Translation:

List of all members.


Class Summary

Synopsis

The Bio::EnsEMBL::Compara::AlignSlice framework is used to map features between species. As the
original Bio::EnsEMBL::Translation might mapped only partially, this module extends the core
Bio::EnsEMBL::Translation module to allow the storage of the mapping of both start end codons.
Both start and end codons might be mapped no, one or several times. At the moment this module
implements a couple of method only, all_start_codon_mappings and all_end_codon_mappings which
return a reference to an array of Bio::EnsEMBL::Compara::AlignSlice::Slice which correspond to
sub-slices of the original Bio::EnsEMBL::Compara::AlignSlice::Slice.

Actual mapping is done by the Bio::EnsEMBL::Compara::AlignSlice::Slice module, this one only
stores the results.

Definition at line 23 of file Translation.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public void add_Attributes ()
public void add_DBEntry ()
public void add_ProteinFeature ()
public Listref all_end_codon_mappings ()
public Listref all_start_codon_mappings ()
public Int cdna_end ()
public Int cdna_start ()
public String created_date ()
public Int dbID ()
public String display_id ()
public Int end ()
public Bio::EnsEMBL::Exon end_Exon ()
public Int genomic_end ()
public Int genomic_start ()
public Listref get_all_Attributes ()
public Hashref get_all_DAS_Features ()
public Listref get_all_DASFactories ()
public Listref get_all_DBEntries ()
public Listref get_all_DBLinks ()
public Listref get_all_DomainFeatures ()
public Listref get_all_object_xrefs ()
public Bio::EnsEMBL::ProteinFeature get_all_ProteinFeatures ()
public Bio::EnsEMBL::SeqEdit get_all_SeqEdits ()
public Listref get_all_xrefs ()
public Boolean is_stored ()
public Int length ()
public void load ()
public String modified_date ()
public Bio::Seq modify_translation ()
public Bio::EnsEMBL::Translation new ()
public Bio::EnsEMBL::Translation new_fast ()
public String seq ()
public String stable_id ()
public Int start ()
public Bio::EnsEMBL::Exon start_Exon ()
public Hashref summary_as_hash ()
public temporary_id ()
public Bio::EnsEMBL::Transcript transcript ()
public void transform ()
public String version ()

Method Documentation

public Listref Bio::EnsEMBL::Compara::AlignSlice::Translation::all_end_codon_mappings ( )
  Arg [1]    : [optional] listref of Bio::EnsEMBL::Compara::AlignSlice::Slice
  Example    : $translation->all_end_codon_mappings($all_end_codon_mappings);
  Example    : my $all_end_codon_mappings = $translation->all_end_codon_mappings();
  Description: getter/setter for the results of the mapping of the original end
               codon on the corresponding Bio::EnsEMBL::Compara::AlignSlice::Slice
  Returntype : listref of Bio::EnsEMBL::Compara::AlignSlice::Slice
  Exceptions :
 
Code:
click to view
public Listref Bio::EnsEMBL::Compara::AlignSlice::Translation::all_start_codon_mappings ( )
  Arg [1]    : [optional] listref of Bio::EnsEMBL::Compara::AlignSlice::Slice
  Example    : $translation->all_start_codon_mappings($all_start_codon_mappings);
  Example    : my $all_start_codon_mappings = $translation->all_start_codon_mappings();
  Description: getter/setter for the results of the mapping of the original start
               codon on the corresponding Bio::EnsEMBL::Compara::AlignSlice::Slice
  Returntype : listref of Bio::EnsEMBL::Compara::AlignSlice::Slice
  Exceptions :
 
Code:
click to view

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