Bio::EnsEMBL::ExternalData::Mole::DBSQL CommentAdaptor
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Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::DBSQL::BaseAdaptor
Bio::EnsEMBL::ExternalData::Mole::Comment
Bio::EnsEMBL::ExternalData::Mole::DBSQL::DBAdaptor
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( deprecate throw warning stack_trace_dump )
Inherit
Bio::EnsEMBL::DBSQL::BaseAdaptor
Synopsis
No synopsis!
Description
No description!
Methods
_columns
No description
Code
_objs_from_sth
No description
Code
_tables
No description
Code
fetch_all_by_Entry
No description
Code
fetch_all_by_dbID_list
No description
Code
fetch_all_by_entry_id
No description
Code
fetch_by_dbID
No description
Code
Methods description
None available.
Methods code
_columnsdescriptionprevnextTop
sub _columns {
  my $self = shift;
  return ( 'cmnt.comment_id', 'cmnt.entry_id',
           'cmnt.comment_key','cmnt.comment_value');
}
_objs_from_sthdescriptionprevnextTop
sub _objs_from_sth {
  my ($self, $sth) = @_;
  my @out;
  my ( $comment_id, $entry_id,
       $comment_key, $comment_value);
  $sth->bind_columns(\$ comment_id,\$ entry_id,\$ 
                      comment_key,\$ comment_value);

  while($sth->fetch()) {
    #print STDERR "$comment_id, $entry_id, $comment_key, $comment_value\n";
push @out, Bio::EnsEMBL::ExternalData::Mole::Comment->new( -adaptor => $self, -dbID => $comment_id, -entry_id => $entry_id, -comment_key => $comment_key || undef, -comment_value => $comment_value || undef, ); } return\@ out; } 1;
}
_tablesdescriptionprevnextTop
sub _tables {
  my $self = shift;
  return (['comment' , 'cmnt']);
}
fetch_all_by_EntrydescriptionprevnextTop
sub fetch_all_by_Entry {
  my $self = shift;
  my $entry = shift;
  my $sth = $self->prepare(
            "SELECT cmnt.comment_id ".
            "FROM comment cmnt ".
            "WHERE cmnt.entry_id = ?");
  $sth->bind_param(1, $entry->dbID, SQL_INTEGER);
  $sth->execute();
  my @commentids;
  while (my $id = $sth->fetchrow) {
    push @commentids, $id;
  }
  $sth->finish();

  #my @obj_ids = map {$_->[0]} @commentids;
my @obj_ids = @commentids; my @comments; foreach my $id (@obj_ids) { my $comment_object = $self->fetch_by_dbID($id); push @comments, $comment_object; } return\@ comments;
}
fetch_all_by_dbID_listdescriptionprevnextTop
sub fetch_all_by_dbID_list {
  my ($self,$id_list_ref) = @_;

  if(!defined($id_list_ref) || ref($id_list_ref) ne 'ARRAY') {
    croak("kill object id list reference argument is required");
  }

  return [] if(!@$id_list_ref);

  my @out;
  #construct a constraint like 't1.table1_id = 123'
my @tabs = $self->_tables; my ($name, $syn) = @{$tabs[0]}; # mysql is faster and we ensure that we do not exceed the max query size by
# splitting large queries into smaller queries of 200 ids
my $max_size = 200; my @id_list = @$id_list_ref; while(@id_list) { my @ids; if(@id_list > $max_size) { @ids = splice(@id_list, 0, $max_size); } else { @ids = splice(@id_list, 0); } my $id_str; if(@ids > 1) { $id_str = " IN (" . join(',', @ids). ")"; } else { $id_str = " = " . $ids[0]; } my $constraint = "${syn}.${name}_id $id_str"; push @out, @{$self->generic_fetch($constraint)}; } return\@ out;
}
fetch_all_by_entry_iddescriptionprevnextTop
sub fetch_all_by_entry_id {
  my ($self, $id) = @_;

  my $sth = $self->prepare(
                  "SELECT cmnt.comment_id ".
                  "FROM comment cmnt ".
                  "WHERE cmnt.entry_id = ?");
  $sth->bind_param(1, $id, SQL_INTEGER);
  $sth->execute();

  my @array = @{$sth->fetchall_arrayref()};
  my @ids = map {$_->[0]} @array;
  my $comment_objs = $self->fetch_all_by_dbID_list(\@ids);
  return $comment_objs;
}
fetch_by_dbIDdescriptionprevnextTop
sub fetch_by_dbID {
  my ($self, $id) = @_;
  my $constraint = "cmnt.comment_id = '$id'";
  my ($comment_obj) = @{ $self->generic_fetch($constraint) };
  return $comment_obj;
}
General documentation
No general documentation available.