Raw content of Bio::EnsEMBL::Pipeline::DBSQL::Finished::DnaAlignFeatureAdaptor
<![CDATA[### Bio::EnsEMBL::Pipeline::DBSQL::Finished::DnaAlignFeatureAdaptor
package Bio::EnsEMBL::Pipeline::DBSQL::Finished::DnaAlignFeatureAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DnaDnaAlignFeature;
use Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw(Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor);
sub store {
my ($self, @feats) = @_;
throw("Must call store with features") if( scalar(@feats) == 0 );
my $seq_region_id;
my $analysis_id;
my $first_dbID;
my $last_dbID;
my @tabs = $self->_tables;
my ($tablename) = @{$tabs[0]};
my $history_table = $tablename.'_history';
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
my $sth = $self->prepare(
"INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end,
seq_region_strand, hit_start, hit_end,
hit_strand, hit_name, cigar_line,
analysis_id, score, evalue, perc_ident, external_db_id, hcoverage)
VALUES (?,?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?)");
my $sth_history = $self->prepare(
"INSERT INTO $history_table (seq_region_id, analysis_id, align_feature_id_start,
align_feature_id_end, db_version , date)
VALUES (?,?,?,?,?,NOW())");
FEATURE: foreach my $feat ( @feats ) {
if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") ) {
throw("feature must be a Bio::EnsEMBL::DnaDnaAlignFeature,"
. " not a [".ref($feat)."].");
}
if($feat->is_stored($db)) {
warning("DnaDnaAlignFeature [".$feat->dbID."] is already stored" .
" in this database.");
next FEATURE;
}
my $hstart = $feat->hstart();
my $hend = $feat->hend();
my $hstrand = $feat->hstrand();
$self->_check_start_end_strand($hstart,$hend, $hstrand);
my $cigar_string = $feat->cigar_string();
if(!$cigar_string) {
$cigar_string = $feat->length() . 'M';
warning("DnaDnaAlignFeature does not define a cigar_string.\n" .
"Assuming ungapped block with cigar_line=$cigar_string .");
}
my $hseqname = $feat->hseqname();
if(!$hseqname) {
throw("DnaDnaAlignFeature must define an hseqname.");
}
if(!defined($feat->analysis)) {
throw("An analysis must be attached to the features to be stored.");
}
#store the analysis if it has not been stored yet
if(!$feat->analysis->is_stored($db)) {
$analysis_adaptor->store($feat->analysis());
}
my $original = $feat;
$analysis_id = $feat->analysis->dbID;
($feat, $seq_region_id) = $self->_pre_store($feat);
$sth->bind_param(1,$seq_region_id,{ TYPE => 'SQL_INTEGER' });
$sth->bind_param(2,$feat->start,{ TYPE => 'SQL_INTEGER' });
$sth->bind_param(3,$feat->end,{ TYPE => 'SQL_INTEGER' });
$sth->bind_param(4,$feat->strand,{ TYPE => 'SQL_TINYINT' });
$sth->bind_param(5,$hstart,{ TYPE => 'SQL_INTEGER' });
$sth->bind_param(6,$hend,{ TYPE => 'SQL_INTEGER' });
$sth->bind_param(7,$hstrand,{ TYPE => 'SQL_TINYINT' });
$sth->bind_param(8,$hseqname,{ TYPE => 'SQL_VARCHAR' });
$sth->bind_param(9,$cigar_string,{ TYPE => 'SQL_LONGVARCHAR' });
$sth->bind_param(10,$analysis_id,{ TYPE => 'SQL_INTEGER' });
$sth->bind_param(11,$feat->score,{ TYPE => 'SQL_DOUBLE' });
$sth->bind_param(12,$feat->p_value,{ TYPE => 'SQL_DOUBLE' });
$sth->bind_param(13,$feat->percent_id,{ TYPE => 'SQL_FLOAT' });
$sth->bind_param(14,$feat->external_db_id,{ TYPE => 'SQL_INTEGER' });
$sth->bind_param(15,$feat->hcoverage,{ TYPE => 'SQL_DOUBLE' });
$sth->execute();
$original->dbID($sth->{'mysql_insertid'});
$original->adaptor($self);
$first_dbID ||= $original->dbID;
$last_dbID = $original->dbID;
}
# save dbIDs, time and db version into history table
$sth_history->execute($seq_region_id,
$analysis_id,
$first_dbID,
$last_dbID,
$self->db_version);
$sth_history->finish();
$sth->finish();
}
sub db_version {
my $self = shift;
$self->{'db_version'} = shift if(@_);
return $self->{'db_version'};
}
1;
]]>