NAME

       Bio::ParameterBaseI - Simple interface class for any parameter-related data such as IDs,
       database name, program arguments, and other odds and ends.

SYNOPSIS

         # Bio::DB::MyParams implements Bio::ParameterBaseI

         @params = (-db   => 'protein',
                    -id   => \@ids,
                    -retmax => 10);

         $pobj->Bio::DB::MyDBParams->new();

         # sets only parameters passed; results in a state change if any parameter
         # passed is new or differs from previously set value

         $pobj->set_params(@params);

         # reset all parameters (sets to undef); results in a state change

         $pobj->reset_params();

         # resets parameters to those in %param (sets all others to undef); resets the
         # object state to indicate change.

         $pobj->reset_params(@params);

         # direct get/set; results in a state change if any parameter passed is new or
         # differs from previously set value

         $pobj->db('nucleotide');
         @ids = $pobj->id();

         # retrieve list containing set defined parameters

         %myparams = $pobj->get_parameters();

         # checks whether the state of the object has changed (i.e. parameter has
         # changed, so on)

         if ($pobj->parameters_changed) {
            # run new search
         } else {
            # return cached search
         }

         # available parameters

         @params = $pobj->available_parameters();

         # retrieve string (URI, query, etc); calling to* methods changes object state
         # to indicate data hasn't changed (so future calls to parameters_changed()
         # will return FALSE)

         $query = $pobj->to_string(); # returns raw string
         $uri = $pobj->to_uri(); #  returns URI-based object
         $uri = $pobj->to_my_data_struct(); #  returns implemenation-specific data structure
         ...

DESCRIPTION

       This is a class interface which focuses on common parameter-related tasks such as building
       simple database queries, URI-related requests, program arguments, etc.

       Implementing classes use the following ways to set parameters:

       1) Create a new instance of a ParameterBaseI-implementing object.

         $pobj->Bio::DB::MyParamClass->new(-db => 'local', -id => \@ids);

       2) Pass the parameters as a hash or array to set_parameters(), which sets the parameters
       listed in the hash but leaves all others as is.

         $pobj->set_parameters(-retmax => 100, -retstart => 20);

       3) Pass the parameters as a hash or array to reset_parameters(), which sets the parameters
       listed in the hash and resets everything else.

         $pobj->reset_parameters(-term => 'pyrimidine'); # sets db and id to undef

       4) Pass values using specific getter/setters.

         $pobj->id(\@ids); # sets IDs

       There is no restriction on what one uses to set up individual parameter getter/setters,
       though there are some other options implemented in BioPerl (for instance,
       Bio::Root::RootI::_set_from_args()).

       A key requirement is there be a way to detect changes in the state of the ParameterBaseI
       object so that any object with a Bio::ParameterBaseI can decide whether to submit a new
       request or return cached data. State changes are revealed by the returned values of the
       parameters_changed() method, which is a simple boolean set to TRUE when the object is
       first instantiated or parameters have changed.

       When retrieving anything using the implementation-specific to_* methods (such as to_query,
       to_string, to_uri, to_request, etc), the ParameterBaseI object state is set to FALSE to
       indicate the data has been accessed and indicate reaccessing will retrieve the same value.
       The observing object can then independently decide whether to rerun the cached query or
       return a previously cached result.

       One can also use indiviual getter/setters to retrieve single parameter values as well as
       use parameter_hash() to retrieve all of the parameters in one go as a hash. To check which
       parameters are available use available_parameters().  Args passed to

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@lists.open-bio.org               - General discussion
         http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists

   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

       Email cjfields at bioperl dot org

APPENDIX

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

   set_parameters
        Title   : set_parameters
        Usage   : $pobj->set_parameters(%params);
        Function: sets the parameters listed in the hash or array
        Returns : None
        Args    : [optional] hash or array of parameter/values.

   reset_parameters
        Title   : reset_parameters
        Usage   : resets values
        Function: resets parameters to either undef or value in passed hash
        Returns : none
        Args    : [optional] hash of parameter-value pairs

   parameters_changed
        Title   : parameters_changed
        Usage   : if ($pobj->parameters_changed) {...}
        Function: Returns boolean true (1) if parameters have changed
        Returns : Boolean (0 or 1)
        Args    : [optional] Boolean

   available_parameters
        Title   : available_parameters
        Usage   : @params = $pobj->available_parameters()
        Function: Returns a list of the available parameters
        Returns : Array of parameters
        Args    : [optional, implementation-dependent] string for returning subset of
                  parameters

   get_parameters
        Title   : get_parameters
        Usage   : %params = $pobj->get_parameters;
        Function: Returns list of key-value pairs of parameter => value
        Returns : List of key-value pairs
        Args    : [optional] A string is allowed if subsets are wanted or (if a
                  parameter subset is default) 'all' to return all parameters

to* methods

       All to_* methods are implementation-specific