Bio::Tools::EUtilities::Summary::DocSum.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::EUtilities::Summary::DocSum - data object for document summary data from esummary

SYNOPSIS

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DESCRIPTION

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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.
   http://bugzilla.open-bio.org/
 
 

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 _

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 remains 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
 
 

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)
 
 

rewind

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

to_string

  Title    : to_string
  Usage    : $foo->to_string()
  Function : converts current object to string
  Returns  : none
  Args     : (optional) simple data for text formatting
  Note     : Used generally for debugging and for various print methods