#
# BioPerl module for Bio::Tools::EUtilities::EUtilDataI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields <cjfields at bioperl dot org>
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::EUtilities::EUtilDataI - eutil data object interface
=head1 SYNOPSIS
# say you had some data in a hash ref ($data) and wanted to create hierarchies
# of object using the same interface, starting with the topmost...
# $object is a Bio::Tools::EUtilities::EUtilDataI instance
$object->_add_data($data);
# in _add_data()... sort through keys and create subobjects as needed
if ($key eq 'foo') {
my $sub = Bio::Tools::EUtilities::FooData->new(-eutil => 'efoo',
-type => 'foo');
$sub->_add_data($subdata);
# store into parent object as needed...
...
}
# access stored data
while (my $sub = $parent->next_Foo) {...}
=head1 DESCRIPTION
This is a simple interface which allows creation of simple typed object
hierarchies. Single layers can be accessed via simple iterators (next_* methods)
or retrieved all at once (get_*) methods; nested data can be iterated through
nested iterators for each object, or retrieved using get_all_* methods.
This interface defines common methods required for all eutil data-holding
objects: _add_data(), eutil(), and type(). It also specifies inheriting
interface classes use at least one of three methods: get_ids(), get_term(), or
get_database(), which are the three types of data that eutils mainly centers on.
Generally, eutil() is the Bio::Tools::EUtilities parser used to set the data.
Similarly, datatype() is the specific data type for the class.
Implementations which rely on subclasses to store data and have iterators should
also define a generalized rewind() method that (by default) rewinds all
iterators to the start. Args passed can specify exactly which iterator to rewind
and (if possible) recursively rewind nested object iterators.
As the method implies, _add_data() is a private method that adds data chunks to
the object and sets internal parameters for the various data objects. Methods
corresponding to the data type simply return the set data or iterate through the
data sets if the values are more complex. Data can alternatively be passed
through the object constructor.
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR
Email cjfields at bioperl dot org
=head1 APPENDIX
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
=cut
package Bio::Tools::EUtilities::EUtilDataI;
use strict;
use warnings;
use Text::Wrap qw(wrap);
use base qw(Bio::Root::RootI);
=head2 eutil
Title : eutil
Usage : $eutil->$foo->eutil
Function : Get/Set eutil
Returns : string
Args : string (eutil)
Throws : on invalid eutil
=cut
{
my %VALID_EUTILS = map {$_ => 1} qw(esearch epost espell egquery elink einfo esummary);
sub eutil {
my ($self, $eutil) = @_;
if ($eutil) {
$self->throw("$eutil not supported") if !exists $VALID_EUTILS{$eutil};
return $self->{'_eutil'} = $eutil;
}
return $self->{'_eutil'};
}
}
=head2 datatype
Title : type
Usage : $type = $qd->datatype;
Function: retrieve simple data type object holds (linkset, docsum, item, etc)
Returns : string (eutil name)
Args : none
Note : this is probably more useful for devs than for users as a way to keep
track of the various types of modules used
=cut
sub datatype {
my $self = shift;
return $self->{'_type'} = shift if @_;
return $self->{'_type'};
}
=head2 rewind
Title : rewind
Usage : $esum->rewind
Function : rewinds the requested iterator
Returns : none
Args : [OPTIONAL] may include 'all', 'recursive', etc.
=cut
sub rewind {
shift->warn("Object may not need an iterator. Please check the documentation.");
}
=head2 _add_data
Title : _add_data
Usage : $foo->_add_data($data)
Function : adds data to current object as a chunk
Returns : none
Args : hash ref containing relevant data
=cut
sub _add_data {
shift->throw_not_implemented;
}
=head2 to_string
Title : to_string
Usage : $foo->to_string()
Function : converts current object to string
Returns : none
Args : (optional) simple data for text formatting
Note : Used generally for debugging and for the print_* methods
=cut
sub to_string {
shift->throw_not_implemented;
}
=head2 _text_wrap
Title : _text_wrap
Usage : $foo->_text_wrap($string)
Function : private internal wrapper for Text::Wrap::wrap
Returns : string
Args : string
Note : Internal use only. Simple wrapper method.
=cut
sub _text_wrap {
shift;
return wrap(@_);
}
1;