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lib/Bio/DB/Das/Chado.pm  view on Meta::CPAN

  my $self = shift;
  my $f_id = shift;

  my @features = $self->features(-feature_id => $f_id);
  return $features[0];
}

*fetch = *get_feature_by_primary_id = \&get_feature_by_feature_id;

sub _complex_search {
    my $self = shift;
    my $name = shift;
    my $class= shift;

    warn "name before wildcard subs:$name\n" if DEBUG;

    $name = "\%$name" unless (0 == index($name, "%"));
    $name = "$name%"  unless (0 == index(reverse($name), "%"));

    warn "name after wildcard subs:$name\n" if DEBUG;

    my $select_part = "select ga.feature_id ";
    my $from_part   = "from gffatts ga ";
    my $where_part  = "where lower(ga.attribute) like ? ";
                                                                                                                          
    if ($class) {
        my $type    = $self->name2term($class);
        return unless $type;
        $from_part .= ", feature f ";
        $where_part.= "and ga.feature_id = f.feature_id and "
                     ."f.type_id = $type";
    }

    $where_part .= " and organism_id = ".$self->organism_id 
        if $self->organism_id;
 
    my $query = $select_part . $from_part . $where_part;
    return ($name, $query);
}

sub _search_name_prep {
  my $self = shift;
  my $name = shift;

  if ($self->fulltext) {

  # For full-text search, the appropriate extension wildcard
  # is ':*' for prefix-matching.  There are limitations to 
  # full-text search in that we cannot find internal parts of
  # words, so wildcards can only come at the ends of phrases/
  # lexemes.  Internal * are converted by tsquery into & [LP]
    $name =~ s/_/\\_/g;             # escape underscores in name
    $name =~ s/(?<=\s)\*//g;        # lose prefix wildcards (word start)
    $name =~ s/(?<=^)\*//g;         # lose prefix wildcards (query start)
    $name =~ s/\*(?=$)/:\*/g;       # convert trailing * (query end) into :*
    $name =~ s/\*(?=\s)/:\*/g;      # convert trailing * (word end) into :*

  }
  else {
    $name =~ s/_/\\_/g;  # escape underscores in name
    $name =~ s/\%/\\%/g; # ditto for percent signs

    $name =~ s/\*/%/g;
  }

  return $name;
}


=head2 srcfeature2name

returns a srcfeature name given a srcfeature_id

=cut

sub srcfeature2name {
    my $self = shift;
    my $id   = shift;

    return $self->{'srcfeature_id'}->{$id} if $self->{'srcfeature_id'}->{$id};

    my $sth = $self->dbh->prepare("select name from feature "
                                 ."where feature_id = ?");
    $sth->execute($id);

    my $hashref = $sth->fetchrow_hashref;
    $self->{'srcfeature_id'}->{$id} = $$hashref{'name'};

    $sth->finish;
    return $self->{'srcfeature_id'}->{$id};
}

=head2 gff_source_db_id

  Title   : gff_source_db_id
  Function: caches the chado db_id from the chado db table

=cut

sub gff_source_db_id {
    my $self = shift;
    return $self->{'gff_source_db_id'} if $self->{'gff_source_db_id'};

    my $sth = $self->dbh->prepare("
       select db_id from db
       where name = 'GFF_source'");
    $sth->execute();

    my $hashref = $sth->fetchrow_hashref;
    $self->{'gff_source_db_id'} = $$hashref{'db_id'}; 

    $sth->finish;
    return $self->{'gff_source_db_id'};
}

=head2 gff_source_dbxref_id

Gets dbxref_id for features that have a gff source associated

=cut