Raw content of Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor
<![CDATA[=head1 NAME
Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor
=head1 SYNOPSIS
=head1 CONTACT
Jessica Severin : jessica@ebi.ac.uk
=head1 APPENDIX
=cut
package Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor;
use Bio::EnsEMBL::Compara::Production::DnaFragChunk;
use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor;
use Bio::EnsEMBL::Compara::DBSQL::SequenceAdaptor;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
#############################
#
# store methods
#
#############################
=head2 store
Arg[1] : one or many DnaFragChunk objects
Example : $adaptor->store($chunk);
Description: stores DnaFragChunk objects into compara database
Returntype : none
Exceptions : none
Caller : general
=cut
sub store {
my ($self, $dfc) = @_;
return unless($dfc);
return unless($dfc->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunk'));
my $query = "INSERT ignore INTO dnafrag_chunk".
"(dnafrag_id,sequence_id,seq_start,seq_end,masking_analysis_data_id) ".
"VALUES (?,?,?,?,?)";
$dfc->sequence_id($self->db->get_SequenceAdaptor->store($dfc->sequence));
if($dfc->masking_analysis_data_id==0 and defined($dfc->masking_options)) {
my $dataDBA = $self->db->get_AnalysisDataAdaptor;
$dfc->masking_analysis_data_id($dataDBA->store($dfc->masking_options));
}
#print("$query\n");
my $sth = $self->prepare($query);
my $insertCount =
$sth->execute($dfc->dnafrag_id, $dfc->sequence_id,
$dfc->seq_start, $dfc->seq_end,
$dfc->masking_analysis_data_id);
if($insertCount>0) {
#sucessful insert
$dfc->dbID( $sth->{'mysql_insertid'} );
$sth->finish;
} else {
$sth->finish;
#UNIQUE(dnafrag_id,seq_start,seq_end,masking_analysis_data_id) prevented insert
#since dnafrag_chunk was already inserted so get dnafrag_chunk_id with select
my $sth2 = $self->prepare("SELECT dnafrag_chunk_id FROM dnafrag_chunk ".
" WHERE dnafrag_id=? and seq_start=? and seq_end=? and masking_analysis_data_id=?");
$sth2->execute($dfc->dnafrag_id, $dfc->seq_start, $dfc->seq_end,
$dfc->masking_analysis_data_id);
my($id) = $sth2->fetchrow_array();
warn("DnaFragChunkAdaptor: insert failed, but dnafrag_chunk_id select failed too") unless($id);
$dfc->dbID($id);
$sth2->finish;
}
$dfc->adaptor($self);
return $dfc;
}
sub update_sequence
{
my $self = shift;
my $dfc = shift;
return 0 unless($dfc);
return 0 unless($dfc->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunk'));
return 0 unless($dfc->dbID);
return 0 unless(defined($dfc->sequence));
return 0 unless(length($dfc->sequence) <= 11500000); #limited by myslwd max_allowed_packet=12M
my $seqDBA = $self->db->get_SequenceAdaptor;
my $newSeqID = $seqDBA->store($dfc->sequence);
return if($dfc->sequence_id == $newSeqID); #sequence unchanged
my $sth = $self->prepare("UPDATE dnafrag_chunk SET sequence_id=? where dnafrag_chunk_id=?");
$sth->execute($newSeqID, $dfc->dbID);
$sth->finish();
$dfc->sequence_id($newSeqID);
return $newSeqID;
}
###############################################################################
#
# fetch methods
#
###############################################################################
=head2 fetch_by_dbID
Arg [1] : int $id
the unique database identifier for the feature to be obtained
Example : $dfc = $adaptor->fetch_by_dbID(1234);
Description: Returns the DnaFragChunk created from the database defined by the
the id $id.
Returntype : Bio::EnsEMBL::Compara::Production::DnaFragChunk
Exceptions : thrown if $id is not defined
Caller : general
=cut
sub fetch_by_dbID{
my ($self,$id) = @_;
unless(defined $id) {
$self->throw("fetch_by_dbID must have an id");
}
my @tabs = $self->_tables;
my ($name, $syn) = @{$tabs[0]};
#construct a constraint like 't1.table1_id = 1'
my $constraint = "${syn}.${name}_id = $id";
#return first element of _generic_fetch list
my ($obj) = @{$self->_generic_fetch($constraint)};
return $obj;
}
=head2 fetch_by_dbIDs
Arg [1...] : int $id (multiple)
the unique database identifier for the feature to be obtained
Example : $dfc = $adaptor->fetch_by_dbID(1234);
Description: Returns an array of DnaFragChunk created from the database defined by the
the id $id.
Returntype : listref of Bio::EnsEMBL::Compara::Production::DnaFragChunk objects
Exceptions : thrown if $id is not defined
Caller : general
=cut
sub fetch_by_dbIDs{
my $self = shift;
my @ids = @_;
return undef unless(scalar(@ids));
my $id_string = join(",", @ids);
my $constraint = "dfc.dnafrag_chunk_id in ($id_string)";
#printf("fetch_by_dbIDs has contraint\n$constraint\n");
#return first element of _generic_fetch list
return $self->_generic_fetch($constraint);
}
=head2 fetch_all
Arg : None
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub fetch_all {
my $self = shift;
return $self->_generic_fetch();
}
=head2 fetch_all_for_genome_db_id
Arg [1] : int $genome_db_id
Example : $chunks = $adaptor->fetch_all_for_genome_db_id(1);
Description: Returns an array with all the DnaFragChunk objects for a given genome_db_id
Returntype : listref of Bio::EnsEMBL::Compara::Production::DnaFragChunk objects
Exceptions : thrown if $id is not defined
Caller : general
=cut
sub fetch_all_for_genome_db_id{
my $self = shift;
my $genome_db_id = shift;
$self->throw() unless (defined $genome_db_id);
my $constraint = "df.genome_db_id='$genome_db_id'";
my $join = [[['dnafrag', 'df'], 'dfc.dnafrag_id=df.dnafrag_id']];
return $self->_generic_fetch($constraint, $join);
}
############################
#
# INTERNAL METHODS
# (pseudo subclass methods)
#
############################
#internal method used in multiple calls above to build objects from table data
sub _tables {
my $self = shift;
return (['dnafrag_chunk', 'dfc'] );
}
sub _columns {
my $self = shift;
return qw (dfc.dnafrag_chunk_id
dfc.dnafrag_id
dfc.seq_start
dfc.seq_end
dfc.masking_analysis_data_id
dfc.sequence_id
);
}
sub _default_where_clause {
my $self = shift;
return '';
}
sub _final_clause {
my $self = shift;
$self->{'_final_clause'} = shift if(@_);
return $self->{'_final_clause'};
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my %column;
$sth->bind_columns( \( @column{ @{$sth->{NAME_lc} } } ));
my @chunks = ();
while ($sth->fetch()) {
my $dfc;
$dfc = Bio::EnsEMBL::Compara::Production::DnaFragChunk->new();
$dfc->adaptor($self);
$dfc->dbID($column{'dnafrag_chunk_id'});
$dfc->seq_start($column{'seq_start'});
$dfc->seq_end($column{'seq_end'});
$dfc->sequence_id($column{'sequence_id'});
$dfc->dnafrag_id($column{'dnafrag_id'});
$dfc->masking_analysis_data_id($column{'masking_analysis_data_id'});
if($column{'masking_analysis_data_id'}) {
$dfc->masking_options($self->_fetch_MaskingOptions_by_dbID($column{'masking_analysis_data_id'}));
#reset masking_analysis_data_id second because setting masking_options internal clears ID
$dfc->masking_analysis_data_id($column{'masking_analysis_data_id'});
}
#$dfc->display_short();
push @chunks, $dfc;
}
$sth->finish;
return \@chunks
}
=head2 _generic_fetch
Arg [1] : (optional) string $constraint
An SQL query constraint (i.e. part of the WHERE clause)
Arg [2] : (optional) string $logic_name
the logic_name of the analysis of the features to obtain
Example : $fts = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall');
Description: Performs a database fetch and returns feature objects in
contig coordinates.
Returntype : listref of Bio::EnsEMBL::Production::DnaFragChunk in contig coordinates
Exceptions : none
Caller : internal
=cut
sub _generic_fetch {
my ($self, $constraint, $join) = @_;
my @tables = $self->_tables;
my $columns = join(', ', $self->_columns());
if ($join) {
foreach my $single_join (@{$join}) {
my ($tablename, $condition, $extra_columns) = @{$single_join};
if ($tablename && $condition) {
push @tables, $tablename;
if($constraint) {
$constraint .= " AND $condition";
} else {
$constraint = " $condition";
}
}
if ($extra_columns) {
$columns .= ", " . join(', ', @{$extra_columns});
}
}
}
#construct a nice table string like 'table1 t1, table2 t2'
my $tablenames = join(', ', map({ join(' ', @$_) } @tables));
my $sql = "SELECT $columns FROM $tablenames";
my $default_where = $self->_default_where_clause;
my $final_clause = $self->_final_clause;
#append a where clause if it was defined
if($constraint) {
$sql .= " WHERE $constraint ";
if($default_where) {
$sql .= " AND $default_where ";
}
} elsif($default_where) {
$sql .= " WHERE $default_where ";
}
#append additional clauses which may have been defined
$sql .= " $final_clause" if($final_clause);
#print STDERR $sql,"\n";
my $sth = $self->prepare($sql);
$sth->execute;
# print STDERR $sql,"\n";
# print STDERR "sql execute finished. about to build objects\n";
return $self->_objs_from_sth($sth);
}
sub _fetch_DnaFrag_by_dbID
{
my $self = shift;
my $dnafrag_id = shift;
return $self->db->get_DnaFragAdaptor->fetch_by_dbID($dnafrag_id);
}
sub _fetch_MaskingOptions_by_dbID
{
my $self = shift;
my $data_id = shift;
$self->{'_masking_cache'} = {} unless(defined($self->{'_masking_cache'}));
if(!defined($self->{'_masking_cache'}->{$data_id})) {
#print("FETCH masking_options for data_id = $data_id\n");
my $dataDBA = new Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor($self->dbc);
$self->{'_masking_cache'}->{$data_id} = $dataDBA->fetch_by_dbID($data_id);
}
return $self->{'_masking_cache'}->{$data_id};
}
1;
]]>