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lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm  view on Meta::CPAN

    map {$_ = $self->unescape($_);} @values;
    if ($Special_attributes{$tag}) {  # reserved attribute
      push @{$reserved{$tag}},@values;
    } else {
      push @{$unreserved{$tag}},@values
    }
  }
  return (\%reserved,\%unreserved);
}

=item start_or_finish_sequence

  $loader->start_or_finish_sequence('Chr9')

This method is called at the beginning and end of a fasta section.

=cut

# sub start_or_finish_sequence { } inherited

=item load_sequence

  $loader->load_sequence('gatttcccaaa')

This method is called to load some amount of sequence after
start_or_finish_sequence() is first called.

=cut

# sub load_sequence { } inherited

=item open_fh

 my $io_file = $loader->open_fh($filehandle_or_path)

This method opens up the indicated file or pipe, using some
intelligence to recognized compressed files and URLs and doing the
right thing.

=cut

# sub open_fh { } inherited

# sub msg { } inherited

=item time

 my $time = $loader->time

This method returns the current time in seconds, using Time::HiRes if available.

=cut

# sub time { } inherited

=item unescape

 my $unescaped = GFF3Loader::unescape($escaped)

This is an internal utility.  It is the same as CGI::Util::unescape,
but doesn't change pluses into spaces and ignores unicode escapes.

=cut

# sub unescape { } inherited

sub _remap {
    my $self = shift;
    my ($ref,$start,$end,$strand) = @_;
    my $mapper = $self->coordinate_mapper;
    return ($ref,$start,$end,$strand) unless $mapper;

    my ($newref,$coords) = $mapper->($ref,[$start,$end]);
    return unless defined $coords->[0];
    if ($coords->[0] > $coords->[1]) {
	@{$coords} = reverse(@{$coords}); 
	$strand *= -1;
    }
    return ($newref,@{$coords},$strand);
}

sub _indexit { # override
    my $self      = shift;
    return $self->{load_data}{Helper}->indexit(@_);
}

sub _local2global { # override
    my $self      = shift;
    return $self->{load_data}{Helper}->local2global(@_);
}

=item local_ids

 my $ids    = $self->local_ids;
 my $id_cnt = @$ids;

After performing a load, this returns an array ref containing all the
load file IDs that were contained within the file just loaded.

=cut

sub local_ids { # override
    my $self = shift;
    return $self->{load_data}{Helper}->local_ids(@_);
}

=item loaded_ids

 my $ids    = $loader->loaded_ids;
 my $id_cnt = @$ids;

After performing a load, this returns an array ref containing all the
feature primary ids that were created during the load.

=cut

sub loaded_ids { # override
    my $self = shift;
    return $self->{load_data}{Helper}->loaded_ids(@_);
}