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BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Root::Storable

NAME

Bio::Root::Storable - object serialisation methods

SYNOPSIS

my $storable = Bio::Root::Storable->new();

# Store/retrieve using class retriever
my $token     = $storable->store();
my $storable2 = Bio::Root::Storable->retrieve( $token );

# Store/retrieve using object retriever
my $storable2 = $storable->new_retrievable();
$storable2->retrieve();

DESCRIPTION

Generic module that allows objects to be safely stored/retrieved from disk. Can be inhereted by any BioPerl object. As it will not usually be the first class in the inheretence list, _initialise_storable() should be called during object instantiation.

Object storage is recursive; If the object being stored contains other storable objects, these will be stored separately, and replaced by a skeleton object in the parent heirarchy. When the parent is later retrieved, its children remain in the skeleton state until explicitly retrieved by the parent. This lazy-retrieve approach has obvious memory efficiency benefits for certain applications.

By default, objects are stored in binary format (using the Perl Storable module). Earlier versions of Perl5 do not include Storable as a core module. If this is the case, ASCII object storage (using the Perl Data::Dumper module) is used instead.

ASCII storage can be enabled by default by setting the value of $Bio::Root::Storable::BINARY to false.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bio.perl.org

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Will Spooner

Email whs@sanger.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Arg [1]   : -workdir  => filesystem path,
            -template => tmpfile template,
            -suffix   => tmpfile suffix,
Function  : Builds a new Bio::Root::Storable inhereting object
Returntype: Bio::Root::Storable inhereting object
Exceptions: 
Caller    : 
Example   : $storable = Bio::Root::Storable->new()

_initialise_storable

Arg [1]   : See 'new' method
Function  : Initialises storable-specific attributes
Returntype: boolean
Exceptions: 
Caller    : 
Example   :

statefile

Arg [1]   : string (optional)
Function  : Accessor for the file to write state into.
            Should not normaly use as a setter - let Root::IO
            do this for you.
Returntype: string
Exceptions: 
Caller    : Bio::Root::Storable->store
Example   : my $statefile = $obj->statefile();

workdir

Arg [1]   : string (optional) (TODO - convert to array for x-platform)
Function  : Accessor for the statefile directory. Defaults to File::Spec->tmpdir
Returntype: string
Exceptions: 
Caller    : 
Example   : $obj->workdir('/tmp/foo');

template

Arg [1]   : string (optional)
Function  : Accessor for the statefile template. Defaults to XXXXXXXX
Returntype: string
Exceptions: 
Caller    : 
Example   : $obj->workdir('RES_XXXXXXXX');

suffix

Arg [1]   : string (optional)
Function  : Accessor for the statefile template.
Returntype: string
Exceptions: 
Caller    : 
Example   : $obj->suffix('.state');

new_retrievable

Arg [1]   : Same as for 'new'
Function  : Similar to store, except returns a 'skeleton' of the calling
            object, rather than the statefile.
            The skeleton can be repopulated by calling 'retrieve'. This
            will be a clone of the original object.
Returntype: Bio::Root::Storable inhereting object
Exceptions: 
Caller    : 
Example   : my $skel = $obj->new_retrievable(); # skeleton 
            $skel->retrieve();                  # clone

retrievable

Arg [1]   : none
Function  : Reports whether the object is in 'skeleton' state, and the
            'retrieve' method can be called.
Returntype: boolean
Exceptions: 
Caller    : 
Example   : if( $obj->retrievable ){ $obj->retrieve }

token

Arg [1]   : None
Function  : Accessor for token attribute
Returntype: string. Whatever retrieve needs to retrieve.
            This base implementation returns the statefile
Exceptions: 
Caller    : 
Example   : my $token = $obj->token();

store

Arg [1]   : none
Function  : Saves a serialised representation of the object structure
            to disk. Returns the name of the file that the object was
            saved to.
Returntype: string

Exceptions: 
Caller    : 
Example   : my $token = $obj->store();

serialise

Arg [1]   : none
Function  : Prepares the the serialised representation of the object.
            Object attribute names starting with '__' are skipped.
            This is useful for those that do not serialise too well
            (e.g. filehandles).
            Attributes are examined for other storable objects. If these
            are found they are serialised separately using 'new_retrievable'
Returntype: string
Exceptions: 
Caller    : 
Example   : my $serialised = $obj->serialise();

retrieve

Arg [1]   : string; filesystem location of the state file to be retrieved
Function  : Retrieves a stored object from disk.
            Note that the retrieved object will be blessed into its original
            class, and not the
Returntype: Bio::Root::Storable inhereting object
Exceptions: 
Caller    : 
Example   : my $obj = Bio::Root::Storable->retrieve( $token );

clone

Arg [1]   : none
Function  : Returns a clone of the calling object
Returntype: Bio::Root::Storable inhereting object
Exceptions: 
Caller    : 
Example   : my $clone = $obj->clone();

remove

Arg [1]   : none
Function  : Clears the stored object from disk
Returntype: boolean
Exceptions: 
Caller    : 
Example   : $obj->remove();

_freeze

Arg [1]   : variable
Function  : Converts whatever is in the the arg into a string.
            Uses either Storable::freeze or Data::Dumper::Dump
            depending on the value of $Bio::Root::BINARY
Returntype: 
Exceptions: 
Caller    : 
Example   :

_thaw

Arg [1]   : string
Function  : Converts the string into a perl 'whatever'.
            Uses either Storable::thaw or eval depending on the
            value of $Bio::Root::BINARY.
            Note; the string arg should have been created with 
            the _freeze method, or strange things may occur!
Returntype: variable
Exceptions: 
Caller    : 
Example   :