Raw content of Bio::EnsEMBL::Pipeline::DBSQL::Finished::DnaAlignFeatureAdaptor ### 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;