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Summary

Bio::EnsEMBL::Pipeline::DBSQL::CompressedDnaAlignFeatureAdaptor - Adaptor for compressed DnaAlignFeatures

Package variables

Included modules

Inherit

Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor

Synopsis

    $cdafa = Bio::EnsEMBL::Pipeline::DBSQL::CompressedDnaAlignFeatureAdaptor->new
      (
       $db_adaptor
      );

    @features = @{$cdafa->fetch_by_Slice($slice)};

    $cdafa->store(@features);

Description

This is an adaptor responsible for the retrieval and storage of
CompressedDnaDnaAlignFeatures from the database. This adaptor inherits most of its
functionality from the DnaAlignFeatureAdaptor and BaseFeatureAdaptor
superclasses. It just overrides the store method to allow a the features to be
compressed

Methods

Methods description

None available.

Methods code

sub new {

  my ( $class, @args ) = @_;
  my $self = $class->SUPER::new(@args);
  return $self;

}

sub store {

  my ($self, @feats) = @_;

  throw("Must call store with features") if( scalar(@feats) == 0 );

  my @tabs = $self->_tables;
  my ($tablename) = @{$tabs[0]};

  my $db = $self->db();
  my $analysis_adaptor = $db->get_AnalysisAdaptor();

  my $sth = $self->prepare
    (
     "UPDATE IGNORE $tablename set evalue = evalue+1 
      WHERE seq_region_id = ? 
      AND seq_region_start = ?
      AND seq_region_end  = ?
      AND seq_region_strand = ?
      AND analysis_id = ?");
  
 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;
    my $seq_region_id;
    ($feat, $seq_region_id) = $self->_pre_store($feat);
    $sth->bind_param(1,$seq_region_id,SQL_INTEGER);
    $sth->bind_param(2,$feat->start,SQL_INTEGER);
    $sth->bind_param(3,$feat->end,SQL_INTEGER);
    $sth->bind_param(4,$feat->strand,SQL_TINYINT);
    $sth->bind_param(5,$feat->analysis->dbID,SQL_INTEGER);
    my $result = $sth->execute();
 #   print " $result \n";
    if ($result eq "0E0"){
      $self->SUPER::store($original);
      return;
    }
    $original->dbID($sth->{'mysql_insertid'});
    $original->adaptor($self);
  }

  $sth->finish();
}

1;

}

General documentation

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