Bio-DB-SeqFeature

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lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

 Title   : types
 Usage   : @type_list = $db->types
 Function: Get all the types in the database
 Returns : array of Bio::DB::GFF::Typename objects
 Args    : none
 Status  : public

=cut

sub types {
    shift->throw_not_implemented;
}

=head2 insert_sequence

 Title   : insert_sequence
 Usage   : $success = $db->insert_sequence($seqid,$sequence_string,$offset)
 Function: Inserts sequence data into the database at the indicated offset
 Returns : true if successful
 Args    : see below
 Status  : public

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

 Usage   : @a = $db->attributes
 Function: Returns list of all known attributes
 Returns : Returns list of all known attributes
 Args    : nothing
 Status  : public

=cut

sub attributes {
    my $self = shift;
    shift->throw_not_implemented;
}


=head2 start_bulk_update,finish_bulk_update

 Title   : start_bulk_update,finish_bulk_update
 Usage   : $db->start_bulk_update
           $db->finish_bulk_update
 Function: Activate optimizations for large number of insertions/updates
 Returns : nothing

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

 Returns : true on success
 Args    : optional boolean flag to erase contents of an existing database
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

This method is the back end for init_database(). It must be
implemented by an adaptor that inherits from
Bio::DB::SeqFeature::Store. It returns true on success. @features = $db->features(-seqid=>'Chr1');

=cut

sub _init_database { shift->throw_not_implemented }

=head2 _store

 Title   : _store
 Usage   : $success = $db->_store($indexed,@objects)
 Function: store seqfeature objects into database
 Returns : true on success
 Args    : a boolean flag indicating whether objects are to be indexed,
           and one or more objects
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

corresponding primary_id. The object is then updated with the
primary_id.

=cut

# _store($indexed,@objs)
sub _store {
  my $self    = shift;
  my $indexed = shift;
  my @objs    = @_;
  $self->throw_not_implemented;
}

=head2 _fetch

 Title   : _fetch
 Usage   : $feature = $db->_fetch($primary_id)
 Function: fetch feature from database
 Returns : feature
 Args    : primary id
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

This method is the back end for fetch(). It accepts a primary_id and
returns a feature object. It must be implemented by the adaptor.

In practice, the implementation will retrieve the serialized
Bio::SeqfeatureI object from the database and pass it to the thaw()
method to unserialize it and synchronize the primary_id.

=cut

# _fetch($id)
sub _fetch { shift->throw_not_implemented }

=head2 _fetch_many

 Title   : _fetch_many
 Usage   : $feature = $db->_fetch_many(@primary_ids)
 Function: fetch many features from database
 Returns : feature
 Args    : primary id
 Status  : private -- does not need to be implemented

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

 Returns : true on success
 Args    : A seqfeature object
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR

This method is called by reindex() to update the searchable indexes
for a feature object that has changed.

=cut

# this is called to index a feature
sub _update_indexes { shift->throw_not_implemented }

=head2 _start_reindexing, _end_reindexing

 Title   : _start_reindexing, _end_reindexing
 Usage   : $db->_start_reindexing()
           $db->_end_reindexing
 Function: flag that a series of reindexing operations is beginning/ending
 Returns : true on success
 Args    : none
 Status  : MAY BE IMPLEMENTED BY AN ADAPTOR (optional)

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR

This is the backend for features(), get_features_by_name(),
get_features_by_location(), etc. Arguments are as described for the
features() method, except that only the named-argument form is
recognized.

=cut

# bottleneck query generator
sub _features { shift->throw_not_implemented }

=head2 _search_attributes

 Title   : _search_attributes
 Usage   : @result_list = $db->_search_attributes("text search string",[$tag1,$tag2...],$limit)
 Function: back end for the search_attributes() method
 Returns : results list
 Args    : as per search_attributes()
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR

See search_attributes() for the format of the results list. The only
difference between this and the public method is that the tag list is
guaranteed to be an array reference.

=cut

sub _search_attributes { shift->throw_not_implemented }

=head2 can_store_parentage

 Title   : can_store_parentage
 Usage   : $flag = $db->can_store_parentage
 Function: return true if this adaptor can store parent/child relationships
 Returns : boolean
 Args    : none
 Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

 Returns : number of children successfully stored
 Args    : parent feature and one or more children
 Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS

If can_store_parentage() returns true, then some store-aware features
(e.g. Bio::DB::SeqFeature) will invoke this method to store
feature/subfeature relationships in a normalized table.

=cut

sub _add_SeqFeature { shift->throw_not_implemented }

=head2 _fetch_SeqFeatures

 Title   : _fetch_SeqFeatures
 Usage   : @children = $db->_fetch_SeqFeatures($parent_feature)
 Function: return the immediate subfeatures of the indicated feature
 Returns : list of subfeatures
 Args    : the parent feature
 Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS

If can_store_parentage() returns true, then some store-aware features
(e.g. Bio::DB::SeqFeature) will invoke this method to retrieve
feature/subfeature relationships from the database.

=cut

# _get_SeqFeatures($parent,@list_of_child_types)
sub _fetch_SeqFeatures {shift->throw_not_implemented }

=head2 _insert_sequence

 Title   : _insert_sequence
 Usage   : $success = $db->_insert_sequence($seqid,$sequence_string,$offset)
 Function: Inserts sequence data into the database at the indicated offset
 Returns : true if successful
 Args    : see below
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR

This is the back end for insert_sequence(). Adaptors must implement
this method in order to store and retrieve nucleotide or protein
sequence.

=cut

sub _insert_sequence   { shift->throw_not_implemented }

# _fetch_sequence() is similar to old dna() method

=head2 _fetch_sequence

 Title   : _fetch_sequence
 Usage   : $sequence = $db->_fetch_sequence(-seq_id=>$seqid,-start=>$start,-end=>$end)
 Function: Fetch the indicated subsequence from the database
 Returns : The sequence string (not a Bio::PrimarySeq object!)
 Args    : see below
 Status  : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR

This is the back end for fetch_sequence(). Adaptors must implement
this method in order to store and retrieve nucleotide or protein
sequence.

=cut

sub _fetch_sequence    { shift->throw_not_implemented }

sub seq {
    my $self     = shift;
    my ($seq_id,$start,$end) = @_;
    if (my $a = $self->dna_accessor) {
	return $a->can('seq')           ? $a->seq($seq_id,$start,$end)
	      :$a->can('fetch_sequence')? $a->fetch_sequence($seq_id,$start,$end)
          : undef;
    }
    else {

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

 Function: Return all sequence IDs contained in database
 Returns : list of sequence Ids
 Args    : none
 Status  : TO BE IMPLEMENTED BY ADAPTOR

This method is invoked by seq_ids() to return all sequence IDs
(coordinate systems) known to the database.

=cut

sub _seq_ids { shift->throw_not_implemented }

=head2 _start_bulk_update,_finish_bulk_update

 Title   : _start_bulk_update, _finish_bulk_update
 Usage   : $db->_start_bulk_update
           $db->_finish_bulk_update
 Function: Activate optimizations for large number of insertions/updates
 Returns : nothing
 Args    : nothing
 Status  : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTOR

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

=item $count = $db-E<gt>_featurecount()

Return the number of features in the database. Needed for scalar
%tied_hash.

=back

=cut

sub _firstid  { shift->throw_not_implemented }
sub _nextid   { shift->throw_not_implemented }
sub _existsid { shift->throw_not_implemented }
sub _deleteid { shift->throw_not_implemented }
sub _clearall { shift->throw_not_implemented }
sub _featurecount { shift->throw_not_implemented }


=head1 Internal Methods

These methods are internal to Bio::DB::SeqFeature::Store and adaptors.

=head2 new_instance

 Title   : new_instance
 Usage   : $db = $db->new_instance()

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

  -type/-types   Feature type of interest or array ref of types
  -bins          Number of bins across region. Defaults to 1000.

Note that this method uses an approximate algorithm that is only
accurate to 500 bp, so when dealing with bins that are smaller than
1000 bp, you may see some shifting of counts between adjacent bins.

=cut

sub coverage_array {
    shift->throw_not_implemented;
}


package Bio::DB::SeqFeature::Store::FeatureIterator;
$Bio::DB::SeqFeature::Store::FeatureIterator::VERSION = '1.7.5';
sub new {
    my $self     = shift;
    my @features = @_;
    return bless \@features,ref $self || $self;
}