Bio-DB-SeqFeature

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

 Returns : true if successful
 Args    : none
 Status  : public

After changing any fields in the feature, call update() to write it to
the database. This is not needed for add_SeqFeature() as update() is
invoked automatically.

=cut

sub update {
  my $self = shift;
  my $store = $self->object_store or return;
  $store->store($self);
}

=head2 get_SeqFeatures

 Title   : get_SeqFeature
 Usage   : @subfeatures = $feature->get_SeqFeatures([@types])
 Function: return subfeatures of this feature

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

  return if $delete; # we don't know how to do this

  my $fh = $self->notes_db;
  my @notes = $obj->get_tag_values('Note') if $obj->has_tag('Note');


  print $fh $_,"\t",pack("u*",$id) or $self->throw("An error occurred while updating note index: $!")
    foreach @notes;
}

sub update_or_delete {
  my $self = shift;
  my ($delete,$db,$key,$id) = @_;
  if ($delete) {
    tied(%$db)->del_dup($key,$id);
  } else {
    $db->{$key} = $id;
  }
}

# these methods return pointers to....

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

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


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

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

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

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;
  }