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lib/EEDB/Chrom.pm  view on Meta::CPAN

    $ts = $te+1;
    if($ts > $end) { last; } #we are done
  }

  my $bioseq = Bio::Seq->new(-id=>$name, -seq=>$seq);
  if($strand eq '-') { $bioseq = $bioseq->revcom; }
  return $bioseq;
}


#################################################
#
# DBObject override methods
#
#################################################

=head2 store

  Description  : store this instance into an EEDB database
                 on return the instance will have the primary_id() set.
  Parameter[1] : a MQdb::Database to store into
  Returntype   : $self or undef if a problem occurred
  Exceptions   : none

=cut

sub store {
  my $self = shift;
  my $db   = shift;
  
  if($db) { $self->database($db); }
  my $dbh = $self->database->get_connection;  
  my $sql = "INSERT ignore INTO chrom (
                chrom_name,
                chrom_type,
                assembly_id,
                chrom_length)
             VALUES(?,?,?,?)";
  my $sth = $dbh->prepare($sql);
  $sth->execute($self->chrom_name,
                $self->chrom_type,
                $self->assembly->id,
                $self->chrom_length);

  my $dbID = $sth->{'mysql_insertid'};
  $sth->finish;
  return undef unless($dbID);
  $self->primary_id($dbID);
  return $self;
}

=head2 update

  Description  : updates the data of this instance. require the Chrom to have been
                 fetched from database. It must have database() and primary_id()
  Returntype   : $self
  Exceptions   : none

=cut

sub update {
  my $self = shift;
  
  return undef unless($self->database and $self->id);
  
  my $dbh = $self->database->get_connection;  
  my $sql = "UPDATE chrom set chrom_length=?, description=?, chrom_type=? where chrom_id=?";
  my $sth = $dbh->prepare($sql);
  $sth->execute($self->chrom_length, 
                $self->description,
                $self->chrom_type,
                $self->id);
  return $self;
}

##### DBObject instance override methods #####

#mapRow is an internal method used by the MappedQuery template machinery
sub mapRow {
  my $self = shift;
  my $rowHash = shift;
  my $dbh = shift;

  $self->primary_id($rowHash->{'chrom_id'});
  $self->chrom_name($rowHash->{'chrom_name'});
  $self->chrom_length($rowHash->{'chrom_length'});
  $self->chrom_type($rowHash->{'chrom_type'});
  
  my $assembly = EEDB::Assembly->fetch_by_id($self->database, $rowHash->{'assembly_id'});
  $self->assembly($assembly);
    
  if($__riken_gsc_chrom_global_should_cache != 0) {
    $__riken_gsc_chrom_global_id_cache->{$self->database() . $self->id} = $self;
    $__riken_gsc_chrom_global_nameasm_cache->{$self->database() . $self->chrom_name. $rowHash->{'assembly_id'}} = $self;
  }
      
  return $self;
}


##### public class methods for fetching by utilizing DBObject framework methods #####

sub fetch_by_id {
  my $class = shift;
  my $db = shift;
  my $id = shift;

  if($__riken_gsc_chrom_global_should_cache != 0) {
    my $chrom = $__riken_gsc_chrom_global_id_cache->{$db . $id};
    if(defined($chrom)) { return $chrom; }
  }
  my $sql = "SELECT * FROM chrom WHERE chrom_id=?";
  return $class->fetch_single($db, $sql, $id);
}

sub fetch_all {
  my $class = shift;
  my $db = shift;
  
  my $sql = "SELECT * FROM chrom";
  return $class->fetch_multiple($db, $sql);