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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.

	 https://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08		Bio::ParameterBaseI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX | to* methods

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