Christopher Fields > BioPerl-1.6.901 > Bio::Tools::EUtilities::Summary::ItemContainerI



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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)


  # 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


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.


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AUTHOR Chris Fields ^

Email cjfields at bioperl dot org


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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) = $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)


 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)
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