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# BioPerl module for Bio::Tools::EUtilities::EUtilDataI
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# Please direct questions and support issues to <bioperl-l@bioperl.org>
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# Cared for by Chris Fields <cjfields at bioperl dot org>
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# Copyright Chris Fields
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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Bio::Tools::EUtilities::EUtilDataI - eutil data object interface
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# say you had some data in a hash ref ($data) and wanted to create hierarchies
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# of object using the same interface, starting with the topmost...
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# $object is a Bio::Tools::EUtilities::EUtilDataI instance
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$object->_add_data($data);
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# in _add_data()... sort through keys and create subobjects as needed
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my $sub = Bio::Tools::EUtilities::FooData->new(-eutil => 'efoo',
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$sub->_add_data($subdata);
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# store into parent object as needed...
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while (my $sub = $parent->next_Foo) {...}
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This is a simple interface which allows creation of simple typed object
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hierarchies. Single layers can be accessed via simple iterators (next_* methods)
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or retrieved all at once (get_*) methods; nested data can be iterated through
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nested iterators for each object, or retrieved using get_all_* methods.
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This interface defines common methods required for all eutil data-holding
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objects: _add_data(), eutil(), and type(). It also specifies inheriting
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interface classes use at least one of three methods: get_ids(), get_term(), or
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get_database(), which are the three types of data that eutils mainly centers on.
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Generally, eutil() is the Bio::Tools::EUtilities parser used to set the data.
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Similarly, datatype() is the specific data type for the class.
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Implementations which rely on subclasses to store data and have iterators should
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also define a generalized rewind() method that (by default) rewinds all
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iterators to the start. Args passed can specify exactly which iterator to rewind
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and (if possible) recursively rewind nested object iterators.
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As the method implies, _add_data() is a private method that adds data chunks to
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the object and sets internal parameters for the various data objects. Methods
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corresponding to the data type simply return the set data or iterate through the
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data sets if the values are more complex. Data can alternatively be passed
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through the object constructor.
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Please direct usage questions or support issues to the mailing list:
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I<bioperl-l@bioperl.org>
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rather than to the module maintainer directly. Many experienced and
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reponsive experts will be able look at the problem and quickly
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address it. Please include a thorough description of the problem
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with code and data examples if at all possible.
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Report bugs to the Bioperl bug tracking system to
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help us keep track the bugs and their resolution.
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Bug reports can be submitted via the web.
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https://redmine.open-bio.org/projects/bioperl/
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Email cjfields at bioperl dot org
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The rest of the documentation details each of the
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object methods. Internal methods are usually
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package Bio::Tools::EUtilities::EUtilDataI;
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use Text::Wrap qw(wrap);
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use base qw(Bio::Root::RootI);
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Usage : $eutil->$foo->eutil
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Function : Get/Set eutil
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Args : string (eutil)
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Throws : on invalid eutil
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my %VALID_EUTILS = map {$_ => 1} qw(esearch epost espell egquery elink einfo esummary);
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my ($self, $eutil) = @_;
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$self->throw("$eutil not supported") if !exists $VALID_EUTILS{$eutil};
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return $self->{'_eutil'} = $eutil;
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return $self->{'_eutil'};
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Usage : $type = $qd->datatype;
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Function: retrieve simple data type object holds (linkset, docsum, item, etc)
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Returns : string (eutil name)
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Note : this is probably more useful for devs than for users as a way to keep
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track of the various types of modules used
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return $self->{'_type'} = shift if @_;
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return $self->{'_type'};
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Usage : $esum->rewind
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Function : rewinds the requested iterator
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Args : [OPTIONAL] may include 'all', 'recursive', etc.
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shift->warn("Object may not need an iterator. Please check the documentation.");
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Usage : $foo->_add_data($data)
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Function : adds data to current object as a chunk
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Args : hash ref containing relevant data
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shift->throw_not_implemented;
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Usage : $foo->to_string()
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Function : converts current object to string
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Args : (optional) simple data for text formatting
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Note : Used generally for debugging and for the print_* methods
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shift->throw_not_implemented;
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Usage : $foo->_text_wrap($string)
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Function : private internal wrapper for Text::Wrap::wrap
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Note : Internal use only. Simple wrapper method.
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Bio/Tools/EUtilities/EUtilDataI.pm
