NAME

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

VERSION

version 1.77

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.

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

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
https://bioperl.org/Support.html    - 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://github.com/bioperl/bio-eutilities/issues

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::EUtilities

perl -MCPAN -e shell
install Bio::EUtilities