Bio::EnsEMBL::Utils::Iterator Class Reference

Public Member Functions
public Bio::EnsEMBL::Utils::Iterator	new ()
protected void	_fetch_next_value_if_needed ()
public Object	next ()
public Boolean	has_next ()
public Object	peek ()
public Bio::EnsEMBL::Utils::Iterator	grep ()
public Bio::EnsEMBL::Utils::Iterator	map ()
public void	each ()
public Arrayref	to_arrayref ()
public Bio::EnsEMBL::Utils::Iterator	append ()
public Bio::EnsEMBL::Utils::Iterator	take ()
public Bio::EnsEMBL::Utils::Iterator	skip ()
public Returntype	reduce ()

Detailed Description

Synopsis

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.

Definition at line 44 of file Iterator.pm.

Member Function Documentation

_fetch_next_value_if_needed()

protected void Bio::EnsEMBL::Utils::Iterator::_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     : Experimental

Code:

append()

public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::Utils::Iterator::append

(

)

  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     : Experimental

Code:

each()

public void Bio::EnsEMBL::Utils::Iterator::each

(

)

  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     : Experimental

Code:

grep()

public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::Utils::Iterator::grep

(

)

  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     : Experimental

Code:

has_next()

public Boolean Bio::EnsEMBL::Utils::Iterator::has_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     : Experimental

Code:

map()

public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::Utils::Iterator::map

(

)

  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     : Experimental

Code:

new()

public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::Utils::Iterator::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

Code:

next()

public Object Bio::EnsEMBL::Utils::Iterator::next

(

)

  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     : Experimental

Code:

peek()

public Object Bio::EnsEMBL::Utils::Iterator::peek

(

)

  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     : Experimental

Code:

reduce()

public Returntype Bio::EnsEMBL::Utils::Iterator::reduce

(

)

  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

Code:

skip()

public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::Utils::Iterator::skip

(

)

  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     : Experimental

Code:

take()

public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::Utils::Iterator::take

(

)

  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     : Experimental

Code:

to_arrayref()

public Arrayref Bio::EnsEMBL::Utils::Iterator::to_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     : Experimental

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Utils/Iterator.pm