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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::Utils::IteratorSYNOPSIS
my $variation_iterator =
$variation_adaptor->fetch_Iterator_by_VariationSet($1kg_set);
while ( my $variation = $variation_iterator->next ) {
# operate on variation object
print $variation->name, "\n";
}DESCRIPTION
Some adaptor methods may return more objects than can fit in memory at once, in these cases
you can fetch an iterator object instead of the usual array reference. The iterator object
allows you to iterate over the set of objects (using the next() method) without loading the
entire set into memory at once. You can tell if an iterator is exhausted with the has_next()
method. The peek() method allows you to fetch the next object from the iterator without
advancing the iterator - this is useful if you want to check some property of en element in
the set while leaving the iterator unchanged.
You can filter and transform an iterator in an analogous way to using map and grep on arrays
using the provided map() and grep() methods. These methods return another iterator, and only
perform the filtering and transformation on each element as it is requested, so again these
can be used without loading the entire set into memory.
Iterators can be combined together with the append() method which merges together the
iterator it is called on with the list of iterators passed in as arguments. This is
somewhat analogous to concatenating arrays with the push function. append() returns a new
iterator which iterates over each component iterator until it is exhausted before moving
on to the next iterator, in the order in which they are supplied to the method.
An iterator can be converted to an array (reference) containing all the elements in the
set with the to_arrayref() method, but note that this array may consume a lot of memory if
the set the iterator is iterating over is large and it is recommended that you do not call
this method unless there is no way of working with each element at a time.METHODS
new
Argument : either a coderef representing the iterator, in which case this
anonymous subroutine is assumed to return the next object in the
set when called and to return undef when the set is exhausted,
or an arrayref, in which case we return an iterator over this
array. If the argument is not defined then we return an 'empty'
iterator that immediately returns undef
Example :
my @dbIDs = fetch_relevant_dbIDs();
my $iterator = Bio::EnsEMBL::Utils::Iterator->new(
sub { return $self->fetch_by_dbID(shift @dbIDs) }
);
NB: this is a very simple example showing how to call the constructor
that would be rather inefficient in practice, real examples should
probably be smarter about batching up queries to minimise trips to
the database. See examples in the Variation API.
Description: Constructor, creates a new iterator object
Returntype : Bio::EnsEMBL::Utils::Iterator instance
Exceptions : thrown if the supplied argument is not the expected
Caller : general
Status : Experimental_fetch_next_value_if_needed
Example : $iterator->_fetch_next_value_if_needed
Description: Helper method used to fill the internal buffer with the next value of the iterator
Returntype : none
Exceptions : none
Caller : general
Status : Experimentalnext
Example : $obj = $iterator->next
Description: returns the next object from this iterator, or undef if the iterator is exhausted
Returntype : Object type will depend on what this iterator is iterating over
Exceptions : none
Caller : general
Status : Experimentalhas_next
Example : if ($iterator->has_next) { my $obj = $iterator->next }
Description: Boolean - true if this iterator has more elements to fetch, false when
it is exhausted
Returntype : boolean
Exceptions : none
Caller : general
Status : Experimentalpeek
Example : $obj = $iterator->peek
Description: returns the next object from this iterator, or undef if the iterator is exhausted,
much like next but does not advance the iterator (so the same object will be
returned on the following call to next or peek)
Returntype : Object type will depend on what this iterator is iterating over
Exceptions : none
Caller : general
Status : Experimentalgrep
Example : my $filtered_iterator = $original_iterator->grep(sub {$_->name =~ /^rs/});
Description: filter this iterator, returning another iterator
Argument : a coderef which returns true if the element should be included in the
filtered set, or false if the element should be filtered out. $_ will be
set locally to each element in turn so you should be able to write a block
in a similar way as for the perl grep function (although it will need to be
preceded with the sub keyword). Otherwise you can pass in a reference to a
subroutine which expects a single argument with the same behaviour.
Returntype : Bio::EnsEMBL::Utils::Iterator
Exceptions : thrown if the argument is not a coderef
Caller : general
Status : Experimentalmap
Example : my $transformed_iterator = $original_iterator->map(sub {$_->name});
Description: transform the elements of this iterator, returning another iterator
Argument : a coderef which returns the desired transformation of each element.
$_ will be set locally set to each original element in turn so you
should be able to write a block in a similar way as for the perl map
function (although it will need to be preceded with the sub keyword).
Otherwise you can pass in a reference to a subroutine which expects a
single argument with the same behaviour.
Returntype : Bio::EnsEMBL::Utils::Iterator
Exceptions : thrown if the argument is not a coderef
Caller : general
Status : Experimentaleach
Example : $iterator->each(sub { print $_->name, "\n"; });
Description: Performs a full iteration of the current iterator instance.
Argument : a coderef which returns the desired transformation of each element.
$_ will be set locally set to each element.
Returntype : None
Exceptions : thrown if the argument is not a coderef
Caller : general
Status : Experimentalto_arrayref
Example : my $arrayref = $iterator->to_arrayref;
Description: return a reference to an array containing all elements from the
iterator. This is created by simply iterating over the iterator
until it is exhausted and adding each element in turn to an array.
Note that this may consume a lot of memory for iterators over
large collections
Returntype : arrayref
Exceptions : none
Caller : general
Status : Experimentalappend
Example : my $combined_iterator = $iterator1->append($iterator2, $iterator3);
Description: return a new iterator that combines this iterator with the others
passed as arguments, this new iterator will iterate over each
component iterator (in the order supplied here) until it is
exhausted and then move on to the next iterator until all are
exhausted
Argument : an array of Bio::EnsEMBL::Utils::Iterator objects
Returntype : Bio::EnsEMBL::Utils::Iterator
Exceptions : thrown if any of the arguments are not iterators
Caller : general
Status : Experimentaltake
Example : my $limited_iterator = $iterator->take(5);
Description: return a new iterator that only iterates over the
first n elements of this iterator
Argument : a positive integer
Returntype : Bio::EnsEMBL::Utils::Iterator
Exceptions : thrown if the argument is negative
Caller : general
Status : Experimentalskip
Example : my $limited_iterator = $iterator->skip(5);
Description: skip over the first n elements of this iterator (and then return
the same iterator for your method chaining convenience)
Argument : a positive integer
Returntype : Bio::EnsEMBL::Utils::Iterator
Exceptions : thrown if the argument is negative
Caller : general
Status : Experimentalreduce
Example : my $tot_length = $iterator->reduce(sub { $_[0] + $_[1]->length }, 0);
Description: reduce this iterator with the provided coderef, using the (optional)
second argument as the initial value of the accumulator
Argument[1]: a coderef that expects 2 arguments, the current accumulator
value and the next element in the set, and returns the next
accumulator value. Unless the optional second argument is
provided the first accumulator value passed in will be the
first element in the set
Argument[2]: (optional) an initial value to use for the accumulator instead
of the first value of the set
Returntype : returntype of the coderef
Exceptions : thrown if the argument is not a coderef
Caller : general
Status : Experimental