Arg [1]    : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor
  Example    : my $cons_ele_adaptor = $constrained_element->adaptor();
  Example    : $cons_ele_adaptor->adaptor($cons_ele_adaptor);
  Description: Getter/Setter for the adaptor this object uses for database
               interaction.
  Returntype : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object
  Exceptions : thrown if $adaptor is not a
               Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object
  Caller     : general

 
  Arg [1]    : listref $alignment_segments [ [ $dnafrag_id, $start, $end, $genome_db_id, $dnafrag_name ], .. ]
  Example    : my $alignment_segments = $constrained_element->alignment_segments();
               $constrained_element->alignment_segments($alignment_segments);
  Description: Getter/Setter for the attribute alignment_segments 
  Returntype : listref  
  Exceptions : returns undef if no ref.alignment_segments
  Caller     : general

  Arg [1]    : integer $dbID
  Example    : my $dbID = $constrained_element->dbID();
  Example    : $constrained_element->dbID(2);
  Description: Getter/Setter for the attribute dbID 
  Returntype : integer
  Exceptions : returns undef if no ref.dbID
  Caller     : general

  Arg [1]    : (optional) int $end
  Example    : $end = $constrained_element->end;
  Example    : $constrained_element->end($end);
  Description: Getter/Setter for the attribute end.
  Returntype : int
  Exceptions : returns undef if no ref.end
  Caller     : object::methodname

  Arg [1]    : The method_link_species_set_object of the original alignment
  Example    : my $out = Bio::AlignIO->newFh(-fh=>\*STDOUT, -format=> "clustalw");
	       my$cons = $ce_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss, $slice);
               foreach my $simple_align(@{ $ce->get_SimpleAlign($prev_mlss, "uc") }) {
			print $out $simple_align;
	       }
  Note       : Where constrained elements occur in overlapping genomic_align_blocks there will be ambiguities
               in associating an alignment with the correct constrined_element_id.
  Description: Rebuilds the constrained element alignment
  Returntype : an arrayref of Bio::SimpleAlign objects
  Exceptions : throw if Arg-1 is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Caller     : object::methodname

  Arg [1]    : integer $method_link_species_set_id
  Example    : $method_link_species_set_id = $constrained_element->method_link_species_set_id;
  Example    : $constrained_element->method_link_species_set_id(3);
  Description: Getter/Setter for the attribute method_link_species_set_id.
  Returntype : integer
  Exceptions : returns undef if no ref.method_link_species_set_id
  Caller     : object::methodname

  Arg [-dbID] : int $dbID (the database ID for 
		the constrained element block for this object)
  Arg [-ADAPTOR]
              : (opt.) Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor $adaptor
                (the adaptor for connecting to the database)
  Arg [-METHOD_LINK_SPECIES_SET_ID]
              : int $mlss_id (the database internal ID for the $mlss)
  Arg [-SCORE]
              : float $score (the score of this alignment)
  Arg [-ALIGNMENT_SEGMENTS]
              : (opt.) listref of listrefs which each contain 5 values 
		[ [ $dnafrag_id, $dnafrag_start, $dnafrag_end, $genome_db_id, $dnafrag_name ], ... ]
		corresponding to the all the species in the constrained element block.
  Arg [-P_VALUE]
              : (opt.) string $p_value (the p_value of this constrained element)
  Arg [-TAXONOMIC_LEVEL]
              : (opt.) string $taxonomic_level (the taxonomic level of the alignments from which the 
		constrained element was derived)
  Arg [-SLICE]
	     : (opt.) Bio::EnsEMBL::Slice object
  Arg [-START]
	     : (opt.) int ($dnafrag_start - Bio::EnsEMBL::Slice->start + 1).
  Arg [-END]
	     : (opt.) int ($dnafrag_end - Bio::EnsEMBL::Slice->start + 1).
  Arg [-REFERENCE_DNAFRAG_ID]
	     : (opt.) int $dnafrag_id of the slice or dnafrag 

  Example    : my $constrained_element =
                   new Bio::EnsEMBL::Compara::ConstrainedElement(
		       -dbID => $constrained_element_id,
                       -adaptor => $adaptor,
                       -method_link_species_set_id => $method_link_species_set_id,
                       -score => 28.2,
                       -alignment_segments => [ [ $dnafrag_id, $dnafrag_start, $dnafrag_end, $genome_db_id, $dnafrag_name ], .. ], 
									#danfarg_[start|end|id] from constrained_element table
                       -p_value => '5.023e-6',
                       -taxonomic_level => "eutherian mammals",
		       -slice => $slice_obj,
		       -start => ( $dnafrag_start - $slice_obj->start + 1),
		       -end => ( $dnafrag_end - $slice_obj->start + 1),
		       -reference_dnafrag_id => $dnafrag_id,
                   );
  Description: Creates a new ConstrainedElement object
  Returntype : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElement
  Exceptions : none
  Caller     : general

  Arg [1]    : float $p_value
  Example    : my $p_value = $constrained_element->p_value();
  Example    : $constrained_element->p_value('5.35242e-105');
  Description: Getter/Setter for the attribute p_value
  Returntype : float 
  Exceptions : returns undef if no ref.p_value
  Caller     : general

  Arg [1]    : (optional) int $reference_dnafrag_id
  Example    : $dnafrag_id = $constrained_element->reference_dnafrag_id;
  Example    : $constrained_element->reference_dnafrag_id($dnafrag_id);
  Description: Getter/Setter for the attribute end.
  Returntype : int
  Exceptions : returns undef if no ref.reference_dnafrag_id 
  Caller     : object::methodname

  Arg [1]    : float $score
  Example    : my $score = $constrained_element->score();
  Example    : $constrained_element->score(16.8);
  Description: Getter/Setter for the attribute score 
  Returntype : float
  Exceptions : returns undef if no ref.score
  Caller     : general

  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Example    : $slice = $constrained_element->slice;
  Example    : $constrained_element->slice($slice);
  Description: Getter/Setter for the attribute slice.
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions : returns undef if no ref.slice
  Caller     : object::methodname

  Arg [1]    : (optional) int $start
  Example    : $start = $constrained_element->start;
  Example    : $constrained_element->start($start);
  Description: Getter/Setter for the attribute start.
  Returntype : int
  Exceptions : returns undef if no ref.start
  Caller     : object::methodname

  Arg [1]    : string $taxonomic_level
  Example    : my $taxonomic_level = $constrained_element->taxonomic_level();
  Example    : $constrained_element->taxonomic_level("eutherian mammals");
  Description: Getter/Setter for the attribute taxonomic_level 
  Returntype : string
  Exceptions : returns undef if no ref.taxonomic_level
  Caller     : general