/ 
BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::EUtilities::Summary::ItemContainerI

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)

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.

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 _

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)