NAME

Bio::Tools::EUtilities::EUtilDataI - EUtil data object interface.

VERSION

version 1.73

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.

eutil

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

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

rewind

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

_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

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

_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.

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 the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://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 of the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR

Chris Fields <cjfields@bioperl.org>

COPYRIGHT

This software is copyright (c) 2006-2013 by Chris Fields.

This software is available under the same terms as the perl 5 programming language system itself.

cpanm Bio::DB::EUtilities

perl -MCPAN -e shell
install Bio::DB::EUtilities