Reference

Bio::Tools::EUtilities::Summary::ItemContainerI(3pm)

Abtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered).

NAME

Bio::Tools::EUtilities::Summary::ItemContainerI - Abtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered).

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

DocSum data, as returned from esummary, normally is a simple list of item-content-content_type groups. However, items can also contain nested data to represent more complex data (such as structural data). This interface describes the basic methods to generically retrieve the next layer of Item data. For convenience classes may describe more specific methods, but they should be defined in terms of this interface and it's 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) = $eutil->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)

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.

  [email protected]               - General discussion
  https://bioperl.org/Support.html    - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected] 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 <[email protected]>

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.

History