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lib/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm  view on Meta::CPAN

     VALUES (?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?,?)");

 FEATURE: foreach my $feat ( @feats ) {
   if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaPepAlignFeature") ) {
     throw("feature must be a Bio::EnsEMBL::DnaPepAlignFeature,"
           . " not a [".ref($feat)."].");
   }

   if($feat->is_stored($db)) {
     warning("PepDnaAlignFeature [".$feat->dbID."] is already stored" .
             " in this database.");
     next FEATURE;
   }

   #sanity check the hstart and hend
   my $hstart  = $feat->hstart();
   my $hend    = $feat->hend();
   $self->_check_start_end_strand($hstart,$hend,1,$feat->hslice);

   my $cigar_string = $feat->cigar_string();
   if(!$cigar_string) {
     $cigar_string = $feat->length() . 'M';
     warning("DnaPepAlignFeature does not define a cigar_string.\n" .
             "Assuming ungapped block with cigar_string=$cigar_string\n");
   }

   my $hseqname = $feat->hseqname();
   if(!$hseqname) {
     throw("DnaPepAlignFeature 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 $slice = $feat->slice();
   if(!defined($slice) || !($slice->isa("Bio::EnsEMBL::Slice") or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
     throw("A slice must be attached to the features to be stored.");
   }

   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->hstart,SQL_INTEGER);
   $sth->bind_param(6,$feat->hend,SQL_INTEGER);
   $sth->bind_param(7,$feat->hseqname,SQL_VARCHAR);
   $sth->bind_param(8,$feat->cigar_string,SQL_LONGVARCHAR);
   $sth->bind_param(9,$feat->analysis->dbID,SQL_INTEGER);
   $sth->bind_param(10,$feat->score,SQL_DOUBLE);
   $sth->bind_param(11,$feat->p_value,SQL_DOUBLE);
   $sth->bind_param(12,$feat->percent_id,SQL_REAL);
   $sth->bind_param(13,$feat->external_db_id,SQL_INTEGER);
   $sth->bind_param(14,$feat->hcoverage,SQL_DOUBLE);
   $sth->bind_param(15,$feat->align_type,SQL_VARCHAR);

   $sth->execute();
   my $dbId = $self->last_insert_id("${tablename}_id", undef, $tablename);
   $original->dbID($dbId);
   $original->adaptor($self);
 }

 $sth->finish();
}


=head2 _objs_from_sth

  Arg [1]    : DBI statement handle $sth
               an exectuted DBI statement handle generated by selecting 
               the columns specified by _columns() from the table specified 
               by _table()
  Example    : @dna_dna_align_feats = $self->_obj_from_hashref
  Description: PROTECTED implementation of superclass abstract method. 
               Creates DnaDnaAlignFeature objects from a DBI hashref
  Returntype : listref of Bio::EnsEMBL::ProteinAlignFeatures
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
  Status     : Stable

=cut

sub _objs_from_sth {
  my ($self, $sth, $mapper, $dest_slice) = @_;

  #
  # This code is ugly because an attempt has been made to remove as many
  # function calls as possible for speed purposes.  Thus many caches and
  # a fair bit of gymnastics is used.
  #

  my $sa = $self->db()->get_SliceAdaptor();
  my $aa = $self->db()->get_AnalysisAdaptor();

  my @features;
  my %analysis_hash;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;

  my (
    $protein_align_feature_id, $seq_region_id,  $seq_region_start,
    $seq_region_end,           $analysis_id,    $seq_region_strand,
    $hit_start,                $hit_end,        $hit_name,
    $cigar_line,               $evalue,         $perc_ident,
    $score,                    $external_db_id, $hcoverage, $align_type,
    $external_db_name,         $external_display_db_name );

  $sth->bind_columns(\(
           $protein_align_feature_id, $seq_region_id,  $seq_region_start,
           $seq_region_end,           $analysis_id,    $seq_region_strand,
           $hit_start,                $hit_end,        $hit_name,

lib/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm  view on Meta::CPAN

            } elsif ($seq_region_start <= $dest_slice_end) {
              # do nothing
            } elsif ($seq_region_end >= $dest_slice_start) {
              $start += $seq_region_len;
              $end += $seq_region_len;

            } elsif ($seq_region_end <= $dest_slice_end) {
              $end += $seq_region_len if $end < 0;

            } elsif ($seq_region_start > $seq_region_end) {
              $end += $seq_region_len;
            }

          } else {

            if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
              # do nothing
            } elsif ($seq_region_start > $seq_region_end) {
              if ($seq_region_start <= $dest_slice_end) {
                $start -= $seq_region_len;
              } elsif ($seq_region_end >= $dest_slice_start) {
                $end += $seq_region_len;
              }
            }
          }
        }

        $seq_region_start = $start;
        $seq_region_end = $end;
        $seq_region_strand *= -1;

      } ## end else [ if ( $dest_slice_strand...)]

      # Throw away features off the end of the requested slice or on
      # different seq_region.
      if ($seq_region_end < 1
          || $seq_region_start > $dest_slice_length
          || ($dest_slice_sr_id != $seq_region_id)) {
        next FEATURE;
      }
      $slice = $dest_slice;
    }

    # Finally, create the new ProteinAlignFeature.
    push(
      @features,
      $self->_create_feature_fast(
        'Bio::EnsEMBL::DnaPepAlignFeature', {
          'slice'        => $slice,
          'start'        => $seq_region_start,
          'end'          => $seq_region_end,
          'strand'       => $seq_region_strand,
          'hseqname'     => $hit_name,
          'hstart'       => $hit_start,
          'hend'         => $hit_end,
          'hstrand'      => 1,                  # dna_pep_align features
                                                # are always hstrand 1
          'score'        => $score,
          'p_value'      => $evalue,
          'percent_id'   => $perc_ident,
          'cigar_string' => $cigar_line,
          'analysis'     => $analysis,
          'adaptor'      => $self,
          'dbID'           => $protein_align_feature_id,
          'external_db_id' => $external_db_id,
          'hcoverage'      => $hcoverage,
          'align_type'     => $align_type,
          'dbname'         => $external_db_name,
          'db_display_name' => $external_display_db_name
        } ) );

  }

  return \@features;
}



sub _tables {
  my $self = shift;

  return (['protein_align_feature', 'paf'], ['external_db','exdb']);
}


sub _columns {
  my $self = shift;

  #warning _objs_from_hashref method depends on ordering of this list 
  return qw( paf.protein_align_feature_id
             paf.seq_region_id
             paf.seq_region_start
             paf.seq_region_end
             paf.analysis_id
             paf.seq_region_strand
             paf.hit_start
             paf.hit_end
             paf.hit_name
             paf.cigar_line
             paf.evalue
             paf.perc_ident
             paf.score
             paf.external_db_id
             paf.hcoverage
             paf.align_type
	     exdb.db_name
	     exdb.db_display_name);
}

sub _left_join{
    return (['external_db',"exdb.external_db_id = paf.external_db_id"]);
}

=head2 list_dbIDs

  Arg [1]    : none
  Example    : @feature_ids = @{$protein_align_feature_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all protein align 
               features in the current db
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.