=head1 NAME Bio::DB::GFF::Adaptor::berkeleydb::iterator - iterator for Bio::DB::GFF::Adaptor::berkeleydb =head1 SYNOPSIS For internal use only =head1 DESCRIPTION This is an internal module that is used by the Bio::DB::GFF in-memory adaptor to return an iterator across a sequence feature query. The object has a single method, next_feature(), that returns the next feature from the query. The method next_seq() is an alias for next_feature(). =head1 BUGS None known yet. =head1 SEE ALSO L, =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut package Bio::DB::GFF::Adaptor::berkeleydb::iterator; use strict; use DB_File qw(R_FIRST R_NEXT); # this module needs to be cleaned up and documented use Bio::Root::Version; *next_seq = \&next_feature; sub new { my $class = shift; my ($data,$callback,$tmpfile) = @_; return bless {data => $data, callback => $callback, tmpfile => $tmpfile, cache => []},$class; } sub next_feature { my $self = shift; return shift @{$self->{cache}} if @{$self->{cache}}; my $data = $self->{data} or return; my $callback = $self->{callback}; my $features; my $db = tied(%$data); my ($key,$value); for (my $status = $db->seq($key,$value,$self->{iter}++ ? R_NEXT : R_FIRST); $status == 0; $status = $db->seq($key,$value,R_NEXT)) { my @feature = split ($;,$value); $features = $callback->(@feature); last if $features; } unless ($features) { $features = $callback->(); undef $self->{data}; undef $self->{cache}; unlink $self->{tmpfile}; } $self->{cache} = $features or return; shift @{$self->{cache}}; } 1;