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Bio::ParameterBaseI(3)User Contributed Perl DocumentatioBio::ParameterBaseI(3)

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.

	 http://bugzilla.open-bio.org/

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

perl v5.14.1			  2011-07-22		Bio::ParameterBaseI(3)
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