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.IX Title "Bio::Tools::EUtilities::Summary::DocSum 3pm"
.TH Bio::Tools::EUtilities::Summary::DocSum 3pm "2012-03-02" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Tools::EUtilities::Summary::DocSum \- data object for document summary data
from esummary
.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) = $foo\->get_type_by_name(\*(Aqbar\*(Aq); # data type from specific Items
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is the basic class for Document Summary data from \s-1NCBI\s0 eUtils, returned
from esummary.  This implements the simple ItemContainerI interface.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@lists.open\-bio.org               \- General discussion
\&  http://www.bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to
help us keep track the bugs and their resolution.
Bug reports can be submitted via the web.
.PP
.Vb 1
\&  https://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR Chris Fields"
.IX Header "AUTHOR Chris Fields"
Email cjfields at bioperl dot org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title    : new
\& Usage    : 
\& Function : 
\& Returns  : 
\& Args     :
.Ve
.SS "get_ids"
.IX Subsection "get_ids"
.Vb 8
\& Title    : get_ids
\& Usage    : my ($id) = $item\->get_ids;
\& Function : returns array or array ref with id
\& Returns  : array or array ref
\& Args     : none
\& Note     : the behavior of this method remains consistent with other
\&            implementations of get_ids(). To retrieve the single DocSum ID
\&            use get_id()
.Ve
.SS "get_id"
.IX Subsection "get_id"
.Vb 5
\& Title    : get_id
\& Usage    : my ($id) = $item\->get_id;
\& Function : returns UID of record
\& Returns  : integer
\& Args     : none
.Ve
.SH "ItemContainerI methods"
.IX Header "ItemContainerI 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) = 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
.SS "rewind"
.IX Subsection "rewind"
.Vb 7
\& Title    : rewind
\& Usage    : $docsum\->rewind();
\& Function : rewinds DocSum iterator
\& Returns  : none
\& Args     : [optional]
\&           \*(Aqrecursive\*(Aq \- rewind all DocSum object layers
\&                         (Items, ListItems, StructureItems)
.Ve
.SS "to_string"
.IX Subsection "to_string"
.Vb 6
\& 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
.Ve