Bio::EnsEMBL::IdMapping TinyFeature
SummaryPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvsRaw content
Summary
Bio::EnsEMBL::IdMapping::TinyFeature - lightweight feature object
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Synopsis
This object isn't instantiated. See objects which inherit from it
(TinyGene, TinyTranscript, etc.) for examples.
Description
This is the base class for the lightweight feature objects used by the
stable Id maping application. For performance reasons, these objects
are instantiated using a new_fast() method. The internal implementation
is an arrayref (rather than the more common hashref), which optimises
memory usage.
There are no adaptors to fetch TinyFeatures from the database. You
rather use the normal feature adaptors and then create the TinyFeatures
from the heavy objects you get. The memory saving will therefore mainly
take effect when serialising and reloading these objects.
Also note that TinyFeatures don't have a slice attached to them - all
location information (where required) is stored on the feature object
directly.
Methods
created_dateDescriptionCode
idDescriptionCode
modified_dateDescriptionCode
new_fastDescriptionCode
stable_idDescriptionCode
to_stringDescriptionCode
versionDescriptionCode
Methods description
created_datecode    nextTop
  Arg[1]      : (optional) String - the feature's stable Id creation date
  Description : Getter/setter for the feature's stable Id creation date.
  Return type : String
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
idcodeprevnextTop
  Arg[1]      : (optional) Int - the feature's internal Id ("dbID")
  Description : Getter/setter for the feature's internal Id.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
modified_datecodeprevnextTop
  Arg[1]      : (optional) String - the feature's stable Id modification date
  Description : Getter/setter for the feature's stable Id modification date.
  Return type : String
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
new_fastcodeprevnextTop
  Arg[1]      : Arrayref $array_ref - the arrayref to bless into the new object 
  Description : Constructor.
  Return type : Bio::EnsEMBL::IdMapping::TinyFeature implementing class
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
stable_idcodeprevnextTop
  Arg[1]      : (optional) String - the feature's stable Id
  Description : Getter/setter for the feature's stable Id.
  Return type : String
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
to_stringcodeprevnextTop
  Example     : print LOG "Created ", $f->to_string, "\n";
  Description : Prints a string representation of the feature for debug
                purposes.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
versioncodeprevnextTop
  Arg[1]      : (optional) Int - the feature's stable Id version
  Description : Getter/setter for the feature's stable Id version.
  Return type : Int
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::Cache
  Status      : At Risk
              : under development
Methods code
created_datedescriptionprevnextTop
sub created_date {
  my $self = shift;
  $self->[3] = shift if (@_);
  return $self->[3];
}
iddescriptionprevnextTop
sub id {
  my $self = shift;
  $self->[0] = shift if (@_);
  return $self->[0];
}
modified_datedescriptionprevnextTop
sub modified_date {
  my $self = shift;
  $self->[4] = shift if (@_);
  return $self->[4];
}
new_fastdescriptionprevnextTop
sub new_fast {
  my $class = shift;
  my $array_ref = shift;
  return bless $array_ref, $class;
}
stable_iddescriptionprevnextTop
sub stable_id {
  my $self = shift;
  $self->[1] = shift if (@_);
  return $self->[1];
}
to_stringdescriptionprevnextTop
sub to_string {
  my $self = shift;
  return $self->id.':'.$self->stable_id.'.'.$self->version;
}


1;
}
versiondescriptionprevnextTop
sub version {
  my $self = shift;
  $self->[2] = shift if (@_);
  return $self->[2];
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.