package Sequence::File;

use strict;
use warnings;
use Carp;

use UNIVERSAL qw(isa);
use base qw(Root Read Write);

=head2 $file->get_entries

Returns all records so far found in the file.

=cut

sub get_entries {
	my ($self) = @_;

	if (exists $self->{__PACKAGE__."entries"}) {
		return @{ $self->{__PACKAGE__."entries"} };
	}
	else { return undef; }
}

=head2 $file->get_entry(@positions);

Retrieves the @position's'th record found in the file or undef if there is no such sequence.

=cut

sub get_entry {
	my ($self, @offsets) = @_;

	if (exists $self->{__PACKAGE__."entries"} and @offsets) {
		return @{ $self->{__PACKAGE__."entries"} }[@offsets];
	}
	else { return undef }
}

=head2 $self->add_entries(@entries)

Adds more entries to the object. Returns the number of entries added to the object. This may be less than those passed if set_max_entries() has been called.

=cut

sub add_entries {
	my ($self, @entries) = @_;
	return unless @entries;

	for (@entries) {
		croak "Adding non Sequence object" unless isa $_, "Sequence";
		$self->_ids($_->id);
		push @{ $self->{__PACKAGE__."entries"} }, $_;
	}

#	my $max = $self->get_max_entries;
#	if (defined $max) {
#		my $exist_size = @{ $self->{__PACKAGE__."entries"} };
#		if ($exist_size > $max) { return 0 }
#		elsif ($exist_size + @entries > $max) {
#			return push @{ $self->{__PACKAGE__."entries"} }, @entries[0..$max - $exist_size];
#		}
#		else {
#			return push @{ $self->{__PACKAGE__."entries"} }, @entries;
#		}
#	}
#	else {
#		return push @{ $self->{__PACKAGE__."entries"} }, @entries;
#	}
}

=head2 $file->get_entry_by_id(/regex/);

Returns all of those entries which have id's that match the regex.

=cut

# Cache of sequence IDs for fast grepping
sub _ids {
	my ($self, $id) = @_;
	if ($id) { push @{ $self->{__PACKAGE__."ids"} }, $id }
	else { return @{ $self->{__PACKAGE__."ids"} } }
}

sub get_entry_by_id {
	my ($self, $id) = @_;
	croak "No id passed" unless defined $id;

	#return grep { $_->id =~ /$id/ } $self->get_entries;

	{
		my @ids = $self->_ids;
		my @indices = grep { $ids[$_] =~ /$id/ } 0..$#ids;
		return $self->get_entry(@indices);
	}
}

=head2 $file->set_max_entries($size);

Limits the storing of $size records. Will prevent the addition of more records, but won't delete existing records in the object if there are already more than $size entries.

=cut

sub set_max_entries {
	my ($self, $size) = @_;

	$self->{__PACKAGE__."max_size"} = $size;
	return $size;
}

=head2 $file->get_max_entries

Accessor for set_max_entries().

=cut

sub get_max_entries {
	my ($self) = @_;
	return $self->{__PACKAGE__."max_size"};
}

=head2 

=cut

sub sub_seq {
	my ($self, $start, $end) = @_;

	croak "Not passed start and end arguments" unless 2 == grep { defined } $start, $end;

	# Produce a new version of myself, in the right namespace
	my ($new_self) = (ref $self)->new;

	for ($self->get_entries) {
		my ($seq) = $_->sub_seq($start, $end);
		$new_self->add_entries($seq);
	}

	return $new_self;
}

1;