Bio::EnsEMBL::Compara::AlignSlice Translation
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Summary
Bio::EnsEMBL::Compara::AlignSlice::Translation - Extension of the Bio::EnsEMBL::Translation
module for the translations mapped on the AlignSlices
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Translation
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw warning info )
Inherit
Bio::EnsEMBL::Translation
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.
Description
No description!
Methods
all_end_codon_mappingsDescriptionCode
all_start_codon_mappingsDescriptionCode
Methods description
all_end_codon_mappingscode    nextTop
  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 :
all_start_codon_mappingscodeprevnextTop
  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 :
Methods code
all_end_codon_mappingsdescriptionprevnextTop
sub all_end_codon_mappings {
  my $self = shift(@_);

  if (@_) {
    $self->{_all_end_codon_mappings} = shift;
  }

  return $self->{_all_end_codon_mappings};
}

1;
}
all_start_codon_mappingsdescriptionprevnextTop
sub all_start_codon_mappings {
  my $self = shift(@_);

  if (@_) {
    $self->{_all_start_codon_mappings} = shift;
  }

  return $self->{_all_start_codon_mappings};
}
General documentation
INHERITANCETop
This module inherits attributes and methods from Bio::EnsEMBL::Translation module
OBJECT ATTRIBUTESTop
AUTHORSTop
Javier Herrero (jherrero@ebi.ac.uk)
COPYRIGHTTop
Copyright (c) 2006. EnsEMBL Team
You may distribute this module under the same terms as perl itself
CONTACTTop
This modules is part of the EnsEMBL project ()
Questions can be posted to the ensembl-dev mailing list: ensembl-dev@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _