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.IX Title "Bio::Tools::EUtilities::Summary::ItemContainerI 3pm"
.TH Bio::Tools::EUtilities::Summary::ItemContainerI 3pm "2018-09-06" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "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).
.SH "VERSION"
.IX Header "VERSION"
version 1.75
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # 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 = $foo\->get_Items_by_name(\*(Aqbar\*(Aq); # Specifically named Items
\&  ($content) = $foo\->get_contents_by_name(\*(Aqbar\*(Aq); # content from specific Items
\&  ($type) = $foo\->get_type_by_name(\*(Aqbar\*(Aq); # data type from specific Items
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SS "next_Item"
.IX Subsection "next_Item"
.Vb 7
\& 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)
\&            \*(Aqflatten\*(Aq \- iterates through a flattened list ala
\&                          get_all_DocSum_Items()
.Ve
.SS "get_Items"
.IX Subsection "get_Items"
.Vb 5
\& Title    : get_Items
\& Usage    : my @items = $docsum\->get_Items
\& Function : returns list of, well, Items
\& Returns  : array of Items
\& Args     : none
.Ve
.SS "get_all_Items"
.IX Subsection "get_all_Items"
.Vb 8
\& Title    : get_all_Items
\& Usage    : my @items = $docsum\->get_all_Items
\& Function : returns flattened list of all Item objects (Items, ListItems,
\&            StructureItems)
\& Returns  : array of Items
\& Args     : none
\& Note     : items are added top\-down (similar order to using nested calls)
\&            in original list order.
\&
\&             1         2        7        8
\&           Item  \-   Item  \-  Item  \-  Item ...
\&                     |
\&                    | 3        6
\&                 ListItem \- ListItem
\&                   |
\&                  | 4          5
\&               Structure \- Structure
.Ve
.SS "get_all_names"
.IX Subsection "get_all_names"
.Vb 5
\& Title    : get_all_names
\& Usage    : my @names = get_all_names()
\& Function : Returns an array of names for all Item(s) in DocSum.
\& Returns  : array of unique strings
\& Args     : none
.Ve
.SS "get_Items_by_name"
.IX Subsection "get_Items_by_name"
.Vb 5
\& Title    : get_Items_by_name
\& Usage    : my @items = get_Items_by_name(\*(AqCreateDate\*(Aq)
\& Function : Returns named Item(s) in DocSum (indicated by passed argument)
\& Returns  : array of Item objects
\& Args     : string (Item name)
.Ve
.SS "get_contents_by_name"
.IX Subsection "get_contents_by_name"
.Vb 6
\& Title    : get_contents_by_name
\& Usage    : my ($data) = $eutil\->get_contents_by_name(\*(AqCreateDate\*(Aq)
\& 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)
.Ve
.SS "get_type_by_name"
.IX Subsection "get_type_by_name"
.Vb 6
\& Title    : get_type_by_name
\& Usage    : my $data = get_type_by_name(\*(AqCreateDate\*(Aq)
\& Function : Returns data type for named Item in DocSum (indicated by
\&            passed argument)
\& Returns  : scalar value (string) if present
\& Args     : string (Item name)
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/%%7Bdist%7D
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Chris Fields <cjfields@bioperl.org>
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
This software is copyright (c) 2006\-2013 by Chris Fields.
.PP
This software is available under the same terms as the perl 5 programming language system itself.