Bio::GMOD::Adaptor - Generic factory for Bio::GMOD::Adaptor::* objects


  my $adaptor = Bio::GMOD::Adaptor->new(-mod => 'WormBase');


Bio::GMOD::Adaptor acts as a generic factor for Bio::GMOD::Adaptor::* objects. You will not interact directly with Bio::GMOD::Adaptor objects.

Bio::GMOD::Adaptor primarily serves to read in default values for common variables. These can be provided by a CGI, hardcoded in the Adaptor object, or supplied as named options to the new() constructor.



Create a new Bio::GMOD::Adaptor::* object. new() reads in default values from the WormBase server. These values will be overridden by like-named key-value pairs passed in the @p array.

Defaults are stored in the object by lower case hash key corresponding to the default name. Adaptor objects are usually housed within other objects, say a Bio::GMOD::Update object. You can always can access to the adaptor object itself by calling

    my $adaptor = $gmod_object->adaptor;

And to access a variable:

    my $value = $adaptor->default_name

Variable names can be populated in one of three ways, or by mixing and matching any of these approaches. In order of precedence, they are:

1. As named arguments passed to new()
   Bio::GMOD::Update->new(-mysql_path => '/usr/local/var');

Options provided in this manner will override like-named variables defined in steps 2 or 3.

2. Via a custom CGI that returns key=value pairs

See, for example, the WormBase defaults cgi in etc/defaults.wormbase.cgi. This approach gives developers additionaly flexibility for end users -- particularly in cases where file system paths on the server-side or data model nuances may be in flux. Users need not have the newest version of the Bio::GMOD module in order to have the most up-to-date data.

The obvious drawback of this approach is that it requires users to be online.

3. Hardcoded in the Adaptor::"Your Mod" module

In reality, you may wish to provide some aspect of each of these approaches to define site-specific variables.


Parse supplied parameters for new variables of those overriding system defaults. Each option will be loaded into the Bio::GMOD::Adaptor::* object with the option name as a key. A corresponding (lowercase) accessor method will also be created.

Returns an ordered list of: ftp_path : full path to the ftp site, including ftp://path/release tmp_path : full path to the temporary directory release : the WSXXX release to fetch dl_only : boolean flag whether the databases should simply be downloaded acedb_path : full path to the acedb data directory mysql_path : full path to the mysql data directory


You can freely define your own variables names in a Bio::GMOD::Adaptor::"Your MOD" subclass for use in, say, a Bio::GMOD::Update::"Your MOD" subclass. These variables will be AUTOLOAD'ed, becoming Bio::GMOD::Adaptor::"Your MOD" (or Bio::GMOD::Adaptor) methods as appropriate.

The following variable names are protected. Some Bio::GMOD modules utilize these variable names to set defaults.

  tmp_path      Full path to the temporary directory
  ftp_site      The FTP host from which to retrieve files
  version       The current version of the MOD of interest (may be
                   a live or development version)
  install_root  The full path to the MOD installation
  rsync_url     The URL of an rsync server, if required
  rsync_module  An rsync module name to sync to

These can always be overridden using the named parameter style of method calls.


None reported.




Todd W. Harris <>.

Copyright (c) 2003-2005 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.