Bio::T...:DocSum(3pm)

📦
version 1.77 · 4 versions
, in debian trixie, ubuntu resolute, ubuntu stonking

💖 NAME 💖

Bio::Tools::EUtilities::Summary::DocSum — bestie, this is the data object for document summary data from esummary. (You'll spot it filed in the user-contributed Perl docs as Bio::T...:DocSum(3pm).)

🌸 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 💅

Okay so this is the basic class for Document Summary data from NCBI eUtils, handed back to you from esummary. It implements the simple ItemContainerI interface. That's the whole vibe. 👑

🎀 new

  • Title : new
  • Usage :
  • Function :
  • Returns :
  • Args :
ngl bestie, every one of these fields is just sitting there empty. Iconic of it, honestly. 💀

🎀 get_ids

  • Title : get_ids
  • Usage : my ($id) = $item->get_ids;
  • Function : hands you an array or an array ref with the id
  • Returns : array or array ref
  • Args : none
  • Note : the behavior of this method stays consistent with the other implementations of get_ids(). If you want the single DocSum ID, you gotta use get_id() instead. ✨

🎀 get_id

  • Title : get_id
  • Usage : my ($id) = $item->get_id;
  • Function : returns the UID of the record
  • Returns : integer
  • Args : none

🌈 ItemContainerI methods 🌈

💜 next_Item

  • Title : next_Item
  • Usage : while (my $item = $docsum->next_Item) {...}
  • Function : iterates through Items (that nested layer of Item)
  • Returns : a single Item
  • Args : [optional] a 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 a 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 a flattened list of all Item objects (Items, ListItems, StructureItems)
  • Returns : array of Items
  • Args : none
  • Note : items get added top-down (similar order to using nested calls), in the original list order. So like:
  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 the Item(s) in the 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 the named Item(s) in the DocSum (the ones you named in the arg you passed)
  • 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 the named Item(s) in the DocSum (again, whatever you passed in)
  • 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 the data type for the named Item in the DocSum (the one you passed in)
  • Returns : scalar value (string) if present
  • Args : string (Item name)

💜 rewind

  • Title : rewind
  • Usage : $docsum->rewind();
  • Function : rewinds the DocSum iterator
  • Returns : none
  • Args : [optional]
    • 'recursive' — rewind all the DocSum object layers (Items, ListItems, StructureItems)

💜 to_string

  • Title : to_string
  • Usage : $foo->to_string()
  • Function : converts the current object to a string
  • Returns : none
  • Args : (optional) simple data for text formatting
  • Note : this one's generally for debugging and for the various print methods 🫶

🫶 FEEDBACK 🫶

🌸 Mailing lists 🌸

User feedback is literally 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, fr fr.

bioperl-l@bioperl.org               - General discussion
https://bioperl.org/Support.html    - 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. So many experienced and responsive 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 so we can 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 <cjfields@bioperl.org>

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.

and that's the whole page, bestie 💅 this was perl v5.40.0, dated 2025-01-27, Bio::T...:DocSum(3pm). slay, go forth and summarise those documents 🌟
📦 where this page comes from