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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq