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

            

              
              
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
            
          

NAME

Bio::EnsEMBL::IdMapping::Serialisable - base class for serialisable objects

SYNOPSIS

            

              
              
# instantiate an object which extends Serialisable
my $object = YourObject->new(
  -DUMP_PATH  => '/tmp',
  -CACHE_FILE => 'object_cache.ser',
);
# serialise object to file
my $filesize = $object->write_to_file;
print LOG "Serialised object to file of size $filesize.\n";
# later, create another object defining the same serialisation
# location. specifying -LOAD_AUTO will automatically load it from the
# serialisation file.
my $object1 = YourObject->new(
  -DUMP_PATH  => '/tmp',
  -CACHE_FILE => 'object_cache.ser',
  -LOAD_AUTO  => 1,
);
# alternatively, manually load the object from file
$object1->load_from_file;
            
          

DESCRIPTION

This is the base class for serialisable objects used by the stable Id mapping. It's essentially an OO wrapper for Storable, providing a method to store (write_to_file(()) and one to retrieve (read_from_file()) serialised objects.

This class is not instantiated itself, but rather extended by implementing classes.

METHODS

            

              
              
new
write_to_file
read_from_file
dump_path
cache_file_name
cache_file
loaded
            
          

new

            

              
              
Arg [DUMP_PATH] : String - path for object serialisation
Arg [CACHE_FILE] : String - filename of serialised object
Arg [AUTO_LOAD] : Boolean - determines whether object should be automatically
                  loaded on instantiation
Description : Constructor.
Return type : Bio::EnsEMBL::IdMapping::Serialisable implementing object
Exceptions  : thrown on missing argument
Caller      : implementing subclass
Status      : At Risk
            : under development
            
          

write_to_file

            

              
              
Example     : my $filesize = $object->write_to_file;
Description : Serialises an object to a file (determined by
              $self->cache_file).
Return type : String - size of serialisation file
Exceptions  : thrown on I/O errors
Caller      : general
Status      : At Risk
            : under development
            
          

read_from_file

            

              
              
Example     : $object->read_from_file;
Description : Reads a serialised object from file (determined by
              $self->cache_file).
Return type : Bio::EnsEMBL::IdMapping::Serialisable implementing object
Exceptions  : thrown on I/O errors
Caller      : general
Status      : At Risk
            : under development
            
          

dump_path

            

              
              
Arg[1]      : String - dump path for serialisation
Example     : $object->dump_path('/tmp');
Description : Getter/setter for the dump path for serialisation.
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development
            
          

cache_file_name

            

              
              
Arg[1]      : String - file name for serialisation
Example     : $object->cache_file_name('object_cache.ser');
Description : Getter/setter for the file name for serialisation.
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development
            
          

cache_file

            

              
              
Example     : my $cache_file = $object->cache_file;
Description : Returns the path and name of the serialised object file.
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development
            
          

loaded

            

              
              
Arg[1]      : Boolean - "loaded" status
Example     : if ($object->loaded) {
                # do something with the object that was loaded from a file
              } else {
                # the object wasn't loaded but is new, so fill it
              }
Description : Indicates whether a given object was loaded from its serialised
              state on disk.
Return type : Boolean - TRUE if loaded from disk, FALSE otherwise
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development