LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

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NAME

Bio::EnsEMBL::IdMapping::TinyFeature - lightweight feature object

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

  new_fast
  id
  stable_id
  version
  created_date
  modified_date
  to_string

new_fast

  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

id

  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

stable_id

  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

version

  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

created_date

  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

modified_date

  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

to_string

  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

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL