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Removing Items In A ListView
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Bio::Tools::EUtilities::Summary::ItemContainerI(3pm) User Contributed Perl Documentation Bio::Tools::EUtilities::Summary::ItemContainerI(3pm) NAME
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) 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
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. 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. https://redmine.open-bio.org/projects/bioperl/ 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 _ 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) = $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) 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) perl v5.14.2 2012-03-02 Bio::Tools::EUtilities::Summary::ItemContainerI(3pm)
