Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

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

SYNOPSIS

         # 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

DESCRIPTION

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

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 one of the Bioperl mailing lists. Your
       participation is much appreciated.

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

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

AUTHOR Chris Fields

       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 _

   new
        Title    : new
        Usage    :
        Function :
        Returns  :
        Args     :

   get_ids
        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()

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

ItemContainerI methods

   next_Item
        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
                                 get_all_DocSum_Items()

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

   get_all_Items
        Title    : get_all_Items
        Usage    : my @items = $docsum->get_all_Items
        Function : returns flattened list of all Item objects (Items, ListItems,
                   StructureItems)
        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

   get_all_names
        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

   get_Items_by_name
        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)

   get_contents_by_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)

   get_type_by_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)

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

   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 various print methods

perl v5.14.2                                2011-12-2Bio::Tools::EUtilities::Summary::DocSum(3pm)