NAME

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

VERSION

version 1.74

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.

bioperl-l@bioperl.org                  - General discussion
http://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 of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/%%7Bdist%7D

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::DB::EUtilities

perl -MCPAN -e shell
install Bio::DB::EUtilities