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


version 1.77


  # 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


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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 <>


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.