Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Compara::ConstrainedElement Class Reference

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Compara::ConstrainedElement;
  
  my $constrained_element = new Bio::EnsEMBL::Compara::ConstrainedElement(
          -adaptor =\> $constrained_element_adaptor,
          -method_link_species_set_id =\> $method_link_species_set_id,
      -reference_dnafrag_id =\> $dnafrag_id,
          -score =\> 56.2,
          -p_value =\> '1.203e-6',
          -alignment_segments =\> [ [$dnafrag1_id, $start, $end, $genome_db_id, $dnafrag1_name ], [$dnafrag2_id, ... ], ... ],
      -taxonomic_level =\> "eutherian mammals",
      );

GET / SET VALUES
  $constrained_element-\>adaptor($constrained_element_adaptor);
  $constrained_element-\>dbID($constrained_element_id);
  $constrained_element-\>method_link_species_set_id($method_link_species_set_id);
  $constrained_element-\>score(56.2);
  $constrained_element-\>p_value('5.62e-9');
  $constrained_element-\>taxonomic_level("eutherian mammals");
  $constrained_element-\>alignment_segments([ [$dnafrag_id, $start, $end, $genome_db_id, $dnafrag_name ], ... ]);
  $constrained_element-\>slice($slice);
  $constrained_element-\>start($constrained_element_start - $slice_start + 1);
  $constrained_element-\>end($constrained_element_end - $slice_start + 1);
  $constrained_element-\>seq_region_start($self-\>slice-\>start + $self-\>{'start'} - 1);
  $constrained_element-\>seq_region_end($self-\>slice-\>start + $self-\>{'end'} - 1);
  $constrained_element-\>strand($strand);
  $constrained_element-\>reference_dnafrag_id($dnafrag_id);

Definition at line 41 of file ConstrainedElement.pm.

Available Methods

public
Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor 
adaptor ()
public Listref alignment_segments ()
public Int dbID ()
public Int end ()
public Bio::SimpleAlign get_SimpleAlign ()
public Int method_link_species_set_id ()
public
Bio::EnsEMBL::Compara::DBSQL::ConstrainedElement 
new ()
public new_fast ()
public Float p_value ()
public Int reference_dnafrag_id ()
public Float score ()
public Int seq_region_end ()
public Int seq_region_start ()
public Bio::EnsEMBL::Slice slice ()
public Int start ()
public Int strand ()
public Hashref summary_as_hash ()
public String taxonomic_level ()

Method Documentation

public Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor Bio::EnsEMBL::Compara::ConstrainedElement::adaptor ( )
  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
 
Code:
click to view
public Listref Bio::EnsEMBL::Compara::ConstrainedElement::alignment_segments ( )
 
  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
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::ConstrainedElement::dbID ( )
  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
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::ConstrainedElement::end ( )
  Arg [1]    : (optional) int $end
  Example    : $end = $constrained_element->end;
  Example    : $constrained_element->end($end);
  Description: Getter/Setter for the attribute end relative to the begining of the slice.
  Returntype : int
  Exceptions : returns undef if no ref.end
  Caller     : object::methodname
 
Code:
click to view
public Bio::SimpleAlign Bio::EnsEMBL::Compara::ConstrainedElement::get_SimpleAlign ( )
  Arg [1]    : The method_link_species_set_object of the original alignment from 
		which the constrained elements were generated
  Example    : my $out = Bio::AlignIO->newFh(-fh=>\*STDOUT, -format=> "clustalw");
	       my $cons = $ce_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss, $slice);
               foreach my $constrained_element(@{ $cons }) {
			my $simple_align = $constrained_element->get_SimpleAlign($orig_mlss, "uc");
			print $out $simple_align;
	       }
  Description: Rebuilds the constrained element alignment
  Returntype : Bio::SimpleAlign object
  Exceptions : throw if Arg-1 is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Caller     : object::methodname
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::ConstrainedElement::method_link_species_set_id ( )
  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
 
public Bio::EnsEMBL::Compara::DBSQL::ConstrainedElement Bio::EnsEMBL::Compara::ConstrainedElement::new ( )
  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 [-STRAND]
	     : (opt.) int (the strand from the genomic_align).
  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),
		       -strand => $strand,
		       -reference_dnafrag_id => $dnafrag_id,
                   );
  Description: Creates a new ConstrainedElement object
  Returntype : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElement
  Exceptions : none
  Caller     : general
 
Code:
click to view
public Bio::EnsEMBL::Compara::ConstrainedElement::new_fast ( )

Undocumented method

Code:
click to view
public Float Bio::EnsEMBL::Compara::ConstrainedElement::p_value ( )
  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
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::ConstrainedElement::reference_dnafrag_id ( )
  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
 
Code:
click to view
public Float Bio::EnsEMBL::Compara::ConstrainedElement::score ( )
  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
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::ConstrainedElement::seq_region_end ( )
  Arg [1]    : (optional) int $seq_region_end
  Example    : $seq_region_end = $constrained_element->seq_region_end
  Example    : $constrained_element->seq_region_end($seq_region_end);
  Description: Getter/Setter for the attribute end relative to the begining of the dnafrag (genomic coords).
  Returntype : int
  Exceptions : returns undef if no ref.seq_region_end
  Caller     : object::methodname
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::ConstrainedElement::seq_region_start ( )
  Arg [1]    : (optional) int $seq_region_start
  Example    : $seq_region_start = $constrained_element->seq_region_start;
  Example    : $constrained_element->seq_region_start($seq_region_start);
  Description: Getter/Setter for the attribute start relative to the begining of the dnafrag (genomic coords).
  Returntype : int
  Exceptions : returns undef if no ref.seq_region_start
  Caller     : object::methodname
 
Code:
click to view
public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::ConstrainedElement::slice ( )
  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
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::ConstrainedElement::start ( )
  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
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::ConstrainedElement::strand ( )
  Arg [1]    : (optional) int $stand$
  Example    : $end = $constrained_element->strand;
  Example    : $constrained_element->end($strand);
  Description: Getter/Setter for the attribute genomic_align strand.
  Returntype : int
  Exceptions : returns undef if no ref.strand
  Caller     : object::methodname
 
Code:
click to view
public Hashref Bio::EnsEMBL::Compara::ConstrainedElement::summary_as_hash ( )
  Example       : $constrained_summary = $constrained_element->summary_as_hash();
  Description   : Retrieves a textual summary of this ConstrainedElement object.
	              Sadly not descended from Feature, so certain attributes must be explicitly requested
  Returns       : hashref of descriptive strings
 
Code:
click to view
public String Bio::EnsEMBL::Compara::ConstrainedElement::taxonomic_level ( )
  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
 
Code:
click to view

The documentation for this class was generated from the following file: