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Summary

Bio::Tools::EUtilities::EUtilDataI - eutil data object interface

Package variables

Included modules

Inherit

Bio::Root::RootI

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) {...}

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. 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. 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/

Methods

Methods description

 Title    : eutil
 Usage    : $eutil->$foo->eutil
 Function : Get/Set eutil
 Returns  : string
 Args     : string (eutil)
 Throws   : on invalid eutil

 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

 Title    : rewind
 Usage    : $esum->rewind
 Function : rewinds the requested iterator
 Returns  : none
 Args     : [OPTIONAL] may include 'all', 'recursive', etc.

 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

 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

 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.

Methods code

sub eutil {

    my ($self, $eutil) = @_;
    if ($eutil) {
        $self->throw("$eutil not supported") if !exists $VALID_EUTILS{$eutil};
        return $self->{'_eutil'} = $eutil; 
    }
    return $self->{'_eutil'}; 
}

}

sub datatype {

    my $self = shift;
    return $self->{'_type'} = shift if @_;
    return $self->{'_type'};

}

sub rewind {

    shift->warn("Object may not need an iterator.  Please check the documentation.");

}

sub _add_data {

    shift->throw_not_implemented;

}

sub to_string {

    shift->throw_not_implemented;

}

sub _text_wrap {

    shift;
    return wrap(@_);
}

1;

}

General documentation

Email cjfields at bioperl dot org

The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _