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

  my @results;
  for my $bin (@bins_in_range) {
    next unless exists $index->{$bin};
    my @found = keys %{$index->{$bin}};
    for my $f (@found) {
      next if $seenit{$f}++;
      my $feature = $self->_fetch($f) or next;
      next if $strand && $feature->strand != $strand;

      if ($range_type eq 'overlaps') {
	next unless $feature->end >= $start && $feature->start <= $end;
      }
      elsif ($range_type eq 'contains') {
	next unless $feature->start >= $start && $feature->end <= $end;
      }
      elsif ($range_type eq 'contained_in') {
	next unless $feature->start <= $start && $feature->end >= $end;
      }

      push @results,$f;
    }
  }
  $self->update_filter($filter,\@results);
}


sub filter_by_name {
  my ($self, $name, $allow_aliases, $filter) = @_;

  my $index = $self->{_index}{name};

  my @names_to_fetch;
  if (my $regexp = $self->glob_match($name)) {
    @names_to_fetch = grep {/^$regexp$/i} keys %{$index};
  } else {
    @names_to_fetch = lc $name;
  }

  my @results;
  for my $n (@names_to_fetch) {
    if ($allow_aliases) {
      push @results,keys %{$index->{$n}};
    } else {
      push @results,grep {$index->{$n}{$_} == 1} keys %{$index->{$n}};
    }
  }
  $self->update_filter($filter,\@results);
}

sub glob_match {
  my ($self, $term) = @_;
  return unless $term =~ /(?:^|[^\\])[*?]/;
  $term =~ s/(^|[^\\])([+\[\]^{}\$|\(\).])/$1\\$2/g;
  $term =~ s/(^|[^\\])\*/$1.*/g;
  $term =~ s/(^|[^\\])\?/$1./g;
  return $term;
}


sub update_filter {
  my ($self, $filter, $results) = @_;
  return unless @$results;

  if (%$filter) {
    my @filtered = grep {$filter->{$_}} @$results;
    %$filter     = map {$_=>1} @filtered;
  } else {
    %$filter     = map {$_=>1} @$results;
  }

}

sub _search_attributes {
  my ($self, $search_string, $attribute_array, $limit) = @_;

  $search_string =~ tr/*?//d;

  my @words = map {quotemeta($_)} $search_string =~ /(\w+)/g;
  my $search = join '|',@words;

  my (%results,%notes);

  my $index  = $self->{_index}{attribute};
  for my $tag (@$attribute_array) {
    my $attributes = $index->{lc $tag};
    for my $value (keys %{$attributes}) {
      next unless $value =~ /$search/i;
      my @ids = keys %{$attributes->{$value}};
      for my $w (@words) {
	my @hits = $value =~ /($w)/ig or next;
	$results{$_} += @hits foreach @ids;
      }
      $notes{$_} .= "$value " foreach @ids;
    }
  }

  my @results;
  for my $id (keys %results) {
    my $hits = $results{$id};
    my $note = $notes{$id};
    $note =~ s/\s+$//;
    my $relevance = 10 * $hits;
    my $feature   = $self->fetch($id);
    my $name      = $feature->display_name or next;
    my $type      = $feature->type;
    push @results,[$name,$note,$relevance,$type,$id];
  }

  return @results;
}

=head2 types

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