++ed by:

1 non-PAUSE user.

Christopher Fields


Bio::Tools::EUtilities::Summary::DocSum - Data object for document summary data from esummary.


version 1.73


  # Implement ItemContainerI

  # $foo is any ItemContainerI (current implementations are DocSum and Item itself)

  while (my $item = $foo->next_Item) { # iterate through contained Items
     # do stuff here

  @items = $foo->get_Items;  # all Items in the container (hierarchy intact)
  @items = $foo->get_all_Items;  # all Items in the container (flattened)
  @items = $foo->get_Items_by_name('bar'); # Specifically named Items
  ($content) = $foo->get_contents_by_name('bar'); # content from specific Items
  ($type) = $foo->get_type_by_name('bar'); # data type from specific Items


This is the basic class for Document Summary data from NCBI eUtils, returned from esummary. This implements the simple ItemContainerI interface.


 Title    : new
 Usage    :
 Function :
 Returns  :
 Args     :


 Title    : get_ids
 Usage    : my ($id) = $item->get_ids;
 Function : returns array or array ref with id
 Returns  : array or array ref
 Args     : none
 Note     : the behavior of this method remains consistent with other
            implementations of get_ids(). To retrieve the single DocSum ID
            use get_id()


 Title    : get_id
 Usage    : my ($id) = $item->get_id;
 Function : returns UID of record
 Returns  : integer
 Args     : none

ItemContainerI methods


 Title    : next_Item
 Usage    : while (my $item = $docsum->next_Item) {...}
 Function : iterates through Items (nested layer of Item)
 Returns  : single Item
 Args     : [optional] single arg (string)
            'flatten' - iterates through a flattened list ala


 Title    : get_Items
 Usage    : my @items = $docsum->get_Items
 Function : returns list of, well, Items
 Returns  : array of Items
 Args     : none


 Title    : get_all_Items
 Usage    : my @items = $docsum->get_all_Items
 Function : returns flattened list of all Item objects (Items, ListItems,
 Returns  : array of Items
 Args     : none
 Note     : items are added top-down (similar order to using nested calls)
            in original list order.

             1         2        7        8
           Item  -   Item  -  Item  -  Item ...
                    | 3        6
                 ListItem - ListItem
                  | 4          5
               Structure - Structure


 Title    : get_all_names
 Usage    : my @names = get_all_names()
 Function : Returns an array of names for all Item(s) in DocSum.
 Returns  : array of unique strings
 Args     : none


 Title    : get_Items_by_name
 Usage    : my @items = get_Items_by_name('CreateDate')
 Function : Returns named Item(s) in DocSum (indicated by passed argument)
 Returns  : array of Item objects
 Args     : string (Item name)


 Title    : get_contents_by_name
 Usage    : my ($data) = get_contents_by_name('CreateDate')
 Function : Returns content for named Item(s) in DocSum (indicated by
            passed argument)
 Returns  : array of values (type varies per Item)
 Args     : string (Item name)


 Title    : get_type_by_name
 Usage    : my $data = get_type_by_name('CreateDate')
 Function : Returns data type for named Item in DocSum (indicated by
            passed argument)
 Returns  : scalar value (string) if present
 Args     : string (Item name)


 Title    : rewind
 Usage    : $docsum->rewind();
 Function : rewinds DocSum iterator
 Returns  : none
 Args     : [optional]
           'recursive' - rewind all DocSum object layers
                         (Items, ListItems, StructureItems)


 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 various print methods


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


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:



Chris Fields <cjfields@bioperl.org>


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.