Raw content of Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkSetAdaptor
package Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkSetAdaptor;
use strict;
use Bio::EnsEMBL::Compara::Production::DnaFragChunk;
use Bio::EnsEMBL::Compara::Production::DnaFragChunkSet;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
#
# STORE METHODS
#
################
=head2 store
Arg [1] : Bio::EnsEMBL::Compara::Production::DnaFragChunkSet
Example :
Description: stores the set of DnaFragChunk objects
Returntype : int dbID of DnaFragChunkSet
Exceptions :
Caller :
=cut
sub store {
my ($self,$chunkSet) = @_;
unless($chunkSet->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunkSet')) {
$self->throw(
"set arg must be a [Bio::EnsEMBL::Compara::Production::DnaFragChunkSet] "
. "not a $chunkSet");
}
my $sth;
my $insertCount=0;
if(defined($chunkSet->description)) {
$sth = $self->prepare("INSERT ignore INTO subset (description) VALUES (?)");
$insertCount = $sth->execute($chunkSet->description);
} else {
$sth = $self->prepare("INSERT ignore INTO subset SET description=NULL");
$insertCount = $sth->execute();
}
if($insertCount>0) {
$chunkSet->dbID( $sth->{'mysql_insertid'} );
}
else {
#print("insert failed, do select\n");
my $sth2 = $self->prepare("SELECT subset_id FROM subset WHERE description=?");
$sth2->execute($chunkSet->description);
my($id) = $sth2->fetchrow_array();
$chunkSet->dbID($id);
$sth2->finish;
}
$sth->finish;
#print("DnaFragChunkSetAdaptor:store() dbID = ", $chunkSet->dbID, "\n");
my @dnafrag_chunkIds = @{$chunkSet->dnafrag_chunk_ids()};
$sth = $self->prepare("INSERT ignore INTO dnafrag_chunk_set (subset_id, dnafrag_chunk_id) VALUES (?,?)");
foreach my $dnafrag_chunk_id (@dnafrag_chunkIds) {
$sth->execute($chunkSet->dbID, $dnafrag_chunk_id) if($dnafrag_chunk_id);
}
$sth->finish;
$chunkSet->adaptor($self);
return $chunkSet->dbID;
}
=head2 store_link
Arg [1] : int $subset_id
Arg [2] : int $dnafrag_chunk_id
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub store_link {
my ($self, $subset_id, $dnafrag_chunk_id) = @_;
return unless($subset_id and $dnafrag_chunk_id);
my $sth = $self->prepare("INSERT ignore INTO dnafrag_chunk_set (subset_id, dnafrag_chunk_id) VALUES (?,?)");
$sth->execute($subset_id, $dnafrag_chunk_id);
$sth->finish;
}
=head2 delete_link
Arg [1] : int $subset_id
Arg [2] : int $dnafrag_chunk_id
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub delete_link {
my ($self, $subset_id, $dnafrag_chunk_id) = @_;
my $sth = $self->prepare("DELETE FROM dnafrag_chunk_set WHERE subset_id=? AND dnafrag_chunk_id=?");
$sth->execute($subset_id, $dnafrag_chunk_id);
$sth->finish;
}
#
# FETCH METHODS
#
################
=head2 fetch_by_dbID
Arg [1] : int $id
the unique database identifier for the feature to be obtained
Example : $feat = $adaptor->fetch_by_dbID(1234);
Description: Returns the feature created from the database defined by the
the id $id.
Returntype : Bio::EnsEMBL::Compara::Production::DnaFragChunkSet
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_set_description
Arg [1] : string $set_description
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub fetch_by_set_description {
my ($self,$set_description) = @_;
unless(defined $set_description) {
$self->throw("fetch_by_set_description must have a description");
}
#construct a constraint like 't1.table1_id = 1'
my $constraint = "s.description = '$set_description'";
#print("fetch_by_set_name contraint:\n$constraint\n");
#return first element of _generic_fetch list
my ($obj) = @{$self->_generic_fetch($constraint)};
return $obj;
}
=head2 fetch_all
Arg : None
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub fetch_all {
my $self = shift;
return $self->_generic_fetch();
}
#
# INTERNAL METHODS
#
###################
=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 = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall');
Description: Performs a database fetch and returns feature objects in
contig coordinates.
Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
Exceptions : none
Caller : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch
=cut
sub _generic_fetch {
my ($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";
my $sth = $self->prepare($sql);
$sth->execute;
# print STDERR $sql,"\n";
return $self->_objs_from_sth($sth);
}
sub _tables {
my $self = shift;
return (['subset', 's'], ['dnafrag_chunk_set', 'sc']);
}
sub _columns {
my $self = shift;
return qw (s.subset_id
s.description
s.dump_loc
sc.subset_id
sc.dnafrag_chunk_id);
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my %column;
$sth->bind_columns( \( @column{ @{$sth->{NAME_lc} } } ));
my @sets = ();
my %setNames;
my %setDnaFragChunkIds;
while ($sth->fetch()) {
my ($subset_id, $name, $dnafrag_chunk_id);
$subset_id = $column{'subset_id'};
$name = $column{'description'};
$dnafrag_chunk_id = $column{'dnafrag_chunk_id'};
if(defined($setDnaFragChunkIds{$subset_id})) {
$setDnaFragChunkIds{$subset_id}->{$dnafrag_chunk_id} = $dnafrag_chunk_id;
}
else {
$setNames{$subset_id} = $name;
$setDnaFragChunkIds{$subset_id} = {};
$setDnaFragChunkIds{$subset_id}->{$dnafrag_chunk_id} = $dnafrag_chunk_id;
}
}
$sth->finish;
my @allSubsetIds = keys(%setNames);
foreach my $subset_id (@allSubsetIds) {
my ($chunkSet, @dnafrag_chunk_id_list, $dnafrag_chunk_id);
@dnafrag_chunk_id_list = keys(%{$setDnaFragChunkIds{$subset_id}});
my $count = scalar(@dnafrag_chunk_id_list);
# print("chunkSet id = $subset_id has $count unique dnafrag_chunk_ids\n");
$chunkSet = new Bio::EnsEMBL::Compara::Production::DnaFragChunkSet
-dbid => $subset_id,
-name => $setNames{$subset_id},
-adaptor => $self;
# print("loading set '" . $setNames{$subset_id} . "' id=$subset_id\n");
@{$chunkSet->{'_dnafrag_chunk_id_list'}} = @dnafrag_chunk_id_list;
push @sets, $chunkSet;
}
return \@sets
}
sub _default_where_clause {
my $self = shift;
return 's.subset_id = sc.subset_id';
}
sub _final_clause {
my $self = shift;
return '';
}
sub _fetch_all_DnaFragChunk_by_ids {
my $self = shift;
my $chunkID_list = shift; #list reference
return $self->db->get_DnaFragChunkAdaptor->fetch_by_dbIDs(@$chunkID_list);
}
1;