Bio::Tools::EUtilities::Summary
DocSum
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Summary
Bio::Tools::EUtilities::Summary::DocSum - data object for document summary data
from esummary
Package variables
No package variables defined.
Included modules
Inherit
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) = $foo->get_type_by_name('bar'); # data type from specific Items
Description
This is the basic class for Document Summary data from NCBI eUtils, returned
from esummary. This implements the simple ItemContainerI interface.
Methods
Methods description
Title : new
Usage :
Function :
Returns :
Args : |
Title : get_ids
Usage : my ($id) = $item->get_ids;
Function : returns array or array ref with id
Returns : array or array ref
Args : none
Note : the behavior of this method remains consistent with other
implementations of get_ids(). To retrieve the single DocSum ID
use get_id() |
Title : get_id
Usage : my ($id) = $item->get_id;
Function : returns UID of record
Returns : integer
Args : none |
Title : rewind
Usage : $docsum->rewind();
Function : rewinds DocSum iterator
Returns : none
Args : [optional]
'recursive' - rewind all DocSum object layers
(Items, ListItems, StructureItems) |
Title : to_string
Usage : $foo->to_string()
Function : converts current object to string
Returns : none
Args : (optional) simple data for text formatting
Note : Used generally for debugging and for various print methods |
Methods code
sub new
{ my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($type) = $self->_rearrange(['DATATYPE'],@args);
$type ||= 'docsum';
$self->eutil('esummary');
$self->datatype($type);
return $self;} | sub get_ids
{ my $self = shift;
return wantarray ? $self->{'_id'} : [$self->{'_id'}];} | sub get_id
{ my $self = shift;
return $self->{'_id'};} | sub rewind
{ my ($self, $request) = @_;
if ($request && $request eq 'all') {
map {$_->rewind('all') } $self->get_Items;
}
delete $self->{"_items_it"};
}
} | sub _add_data
{ my ($self, $data) = @_;
if ($data->{Item}) {
$self->{'_id'} = $data->{Id} if exists $data->{Id};
for my $sd (@{ $data->{Item} } ) {
$sd->{Id} = $data->{Id} if exists $data->{Id};
my $subdoc =
Bio::Tools::EUtilities::Summary::Item->new(-datatype => 'item',
-verbose => $self->verbose);
$subdoc->_add_data($sd);
push @{ $self->{'_items'} }, $subdoc;
}
}
$self->{'_id'} = $data->{Id} if exists $data->{Id};} | sub to_string
{ my $self = shift;
my $string = sprintf("%-20s%s\n",'UID', ':'.$self->get_id);
while (my $item = $self->next_Item) {
$string .= $item->to_string;
}
return $string;
}
1;} | General documentation
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
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.
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/
Email cjfields at bioperl dot org
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
| ItemContainerI methods | Top |
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()
Title : get_Items
Usage : my @items = $docsum->get_Items
Function : returns list of, well, Items
Returns : array of Items
Args : none
Title : get_all_Items
Usage : my @items = $docsum->get_all_Items
Function : returns flattened list of all Item objects (Items, ListItems,
StructureItems)
Returns : array of Items
Args : none
Note : items are added top-down (similar order to using nested calls)
in original list order.
1 2 7 8
Item - Item - Item - Item ...
|
| 3 6
ListItem - ListItem
|
| 4 5
Structure - Structure
Title : get_all_names
Usage : my @names = get_all_names()
Function : Returns an array of names for all Item(s) in DocSum.
Returns : array of unique strings
Args : none
Title : get_Items_by_name
Usage : my @items = get_Items_by_name('CreateDate')
Function : Returns named Item(s) in DocSum (indicated by passed argument)
Returns : array of Item objects
Args : string (Item name)
Title : get_contents_by_name
Usage : my ($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)
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)