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

NAME

Bio::Tools::EUtilities::Summary::Item - Simple layered object for DocSum item data.

VERSION

version 1.77

SYNOPSIS

  # Items can be nested up to three levels at this time. These levels can be
  # accessed via Item, ListItem, or StructureItem methods:
  while (my $item = $docsum->next_Item) {
     print "Name: ",$item->get_name,"\n";
     print "Data: ",$item->get_content,"\n";
     print "Type: ",$item->get_type,"\n";
     while (my $ls = $item->next_ListItem) {
        # do same here
        while (my $struct = $ls->next_StructureItem) {
           # do more stuff here
        }
     }
  }

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). Up to three nested layers may appear in any document summary.

This class contains methods to access data that can appear in a docsum for any individual item as well as describes methods to traverse the hierarchy of items present in a document summary.

The unique name for items are accessed via get_name(), the content by get_content() (if present), and the data type by get_type(). Items can have ListItems (Item objects with a datatype() 'list'), which in turn can have StructureItems (Item objects with a datatype of 'structure'). Items are initially traversed via a DocSum object using next_Item() or obtained all at once with get_Items(). Similarly, nested Items can be accessed by using next_ListItem/get_ListItems and next_StructureItem/get_StructureItem. A flattened list of items can be accessed with get_all_Items().

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 is to remain 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

next_ListItem

 Title    : next_ListItem
 Usage    : while (my $ls = $item->next_ListItem) {...}
 Function : iterates through ListItems (nested layer of Item)
 Returns  : single ListItem
 Args     : none

get_ListItems

 Title    : get_ListItems
 Usage    : my @ls = $item->get_ListItems
 Function : returns list of, well, List Items
 Returns  : array of List Items
 Args     : none

next_StructureItem

 Title    : next_StructureItem
 Usage    : while (my $struc = $ls->next_StructureItem) {...}
 Function : iterates through StructureItems (nested layer of ListItem)
 Returns  : single StructureItems
 Args     : none

get_StructureItems

 Title    : get_StructureItems
 Usage    : my @structs = $ls->get_StructureItems
 Function : returns list of Structure Items
 Returns  : array of StructureItems
 Args     : none

next_subItem

 Title    : next_subItem
 Usage    : while (my $it = $ls->next_subItem) {...}
 Function : iterates through the next layer of Items
 Returns  : single Item
 Args     : none
 Notes    : unlike next_ListItem and next_StructureItem, this generically
            accesses any sub Items (useful for recursive calls, for example)

get_subItems

 Title    : get_subItems
 Usage    : my @items = $ls->get_subItems
 Function : returns list of sub Items
 Returns  : array of Items
 Args     : none
 Notes    : unlike get_ListItems and get_StructureItems, this generically
            accesses any sub Items (useful for recursive calls, for example)

get_name

 Title    : get_name
 Usage    : my $nm = $ls->get_name
 Function : retrieves Item/ListItem/StructureItem name for this Item
 Returns  : string
 Args     : none

get_type

 Title    : get_type
 Usage    : my $type = $ls->get_type
 Function : retrieves Item/ListItem/StructureItem type
 Returns  : string
 Args     : none
 Note     : this is not the same as the datatype(), which describes the
            group this Item object belongs to

get_content

 Title    : get_content
 Usage    : my $data = $ls->get_content
 Function : retrieves Item/ListItem/StructureItem content (if any)
 Returns  : string
 Args     : none

rewind

 Title    : rewind
 Usage    : $item->rewind()
 Function : rewinds iterators
 Returns  : none
 Args     : [optional] No arg - only rewinds current layer
           'all' - rewind all DocSum object layers
                (Items, ListItems, StructureItems)

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)

to_string

 Title    : to_string
 Usage    : $foo->to_string()
 Function : converts current object to string
 Returns  : none
 Args     : (optional) simple data for text formatting.  This implementation
            passes an argument for layering Items/subItems
 Note     : Used generically for debugging and print_DocSums 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.

  [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 available under the same terms as the perl 5 programming language system itself.