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Bio::Tools::EUtilities::EUtilDataI.3pm

NAME

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

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.

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.

   http://bugzilla.open-bio.org/
 
 

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 _

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.