Inheritance diagram for Bio::EnsEMBL::Exon:

Public Member Functions
public Bio::EnsEMBL::Exon	new ()

public Int	end_phase ()

public Int	phase ()

public Int	frame ()

public Int	start ()

public Int	end ()

public Int	strand ()

public Int	cdna_start ()

public Int	cdna_end ()

public Int	cdna_coding_start ()

public Int	cdna_coding_end ()

public Int	coding_region_start ()

public Int	coding_region_end ()

public Int	rank ()

public Bio::EnsEMBL::Slice	slice ()

public Boolean	equals ()

public void	move ()

public Bio::EnsEMBL::Exon	transform ()

public Bio::EnsEMBL::Exon	transfer ()

public void	add_supporting_features ()

public	flush_supporting_features ()

public Listreference	get_all_supporting_features ()

public void	find_supporting_evidence ()

public String	stable_id ()

public String	created_date ()

public String	modified_date ()

public String	version ()

public String	stable_id_version ()

public Int	is_current ()

public Int	is_constitutive ()

public Int	is_coding ()

public Bio::EnsEMBL::Exon	adjust_start_end ()

public Bio::Seq	peptide ()

protected Bio::EnsEMBL::Mapper::Coordinate	_merge_ajoining_coords ()

public Bio::Seq	seq ()

public String	hashkey ()

public String	display_id ()

public Nothing	load ()

public Hashref	summary_as_hash ()

Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()

public Int	start ()

public Int	end ()

public Int	strand ()

public void	move ()

public Int	length ()

public Bio::EnsEMBL::Analysis	analysis ()

public Bio::EnsEMBL::Slice	slice ()

public Boolean Or Undef	equals ()

public Bio::EnsEMBL::Feature	transform ()

public Bio::EnsEMBL::Feature	transfer ()

public Listref	project_to_slice ()

public Listref	project ()

public String	seqname ()

public String	display_id ()

public String	version ()

public Bio::EnsEMBL::Slice	feature_Slice ()

public String	seq_region_name ()

public Int	seq_region_length ()

public Boolean	seq_region_strand ()

public Int	seq_region_start ()

public Int	seq_region_end ()

public String	coord_system_name ()

public String	seq ()

public Listref	get_all_alt_locations ()

public Boolean	overlaps ()

public Boolean	overlaps_local ()

public List	get_overlapping_Genes ()

public Bio::EnsEMBL::Gene	get_nearest_Gene ()

public String	feature_so_acc ()

public String	feature_so_term ()

public Hashref	summary_as_hash ()

public String	species ()

public	sub_SeqFeature ()

public	add_sub_SeqFeature ()

public	flush_sub_SeqFeature ()

Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()

public Instance	new_fast ()

public Int	dbID ()

public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()

public Boolean	is_stored ()

public	get_all_DAS_Features ()

Detailed Description

Synopsis

  $exon = new Bio::EnsEMBL::Exon(
    -START     => 100,
    -END       => 200,
    -STRAND    => 1,
    -SLICE     => $slice,
    -DBID      => $dbID,
    -ANALYSIS  => $analysis,
    -STABLE_ID => 'ENSE000000123',
    -VERSION   => 2
  );
 
# seq() returns a Bio::Seq
my $seq = $exon->seq->seq();
 
# Peptide only makes sense within transcript context
my $pep = $exon->peptide($transcript)->seq();
 
# Normal feature operations can be performed:
$exon = $exon->transform('clone');
$exon->move( $new_start, $new_end, $new_strand );
print $exon->slice->seq_region_name();

Description

This is a class which represents an exon which is part of a transcript.
See Bio::EnsEMBL:Transcript

Definition at line 42 of file Exon.pm.

Member Function Documentation

◆ _merge_ajoining_coords()

protected Bio::EnsEMBL::Mapper::Coordinate Bio::EnsEMBL::Exon::_merge_ajoining_coords ( )

 
   Arg [1]     : ArrayRef of Bio::EnsEMBL::Mapper::Coordinate objects
   Example     :

   Description : Merges coords which are ajoining or overlapping
   Returntype  : Bio::EnsEMBL::Mapper::Coordinate or undef if it cannot happen
   Exceptions  : Exception if the cooords cannot be condensed into one location
   Caller      : internal
   Status      : Development

Code:

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◆ add_supporting_features()

public void Bio::EnsEMBL::Exon::add_supporting_features ( )

  Arg [1]    : Bio::EnsEMBL::Feature $feature
  Example    :

$exon->add_supporting_features(@features);

  Description: Adds a list of supporting features to this exon. 
               Duplicate features are not added.  
               If supporting features are added manually in this
               way, prior to calling get_all_supporting_features then the
               get_all_supporting_features call will not retrieve supporting
               features from the database.
  Returntype : none
  Exceptions : throw if any of the features are not Feature
               throw if any of the features are not in the same coordinate
               system as the exon
  Caller     : general
  Status     : Stable

Code:

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◆ adjust_start_end()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::Exon::adjust_start_end ( )

  Arg  1     : int $start_adjustment
  Arg  2     : int $end_adjustment
  Example    :

none

  Description: returns a new Exon with this much shifted coordinates
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : none
  Caller     : Transcript->get_all_translateable_Exons()
  Status     : Stable

Code:

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◆ cdna_coding_end()

public Int Bio::EnsEMBL::Exon::cdna_coding_end ( )

    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                  The transcript for which cDNA coordinates should be
                  relative to.
    Example     :

$cdna_coding_end = $exon->cdna_coding_end($transcript);

    Description : Returns the end position of the coding region of the
                  exon in cDNA coordinates.  Returns undef if the whole
                  exon is non-coding.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer or undef
    Exceptions  : Throws if the given argument is not a transcript.
    Caller      : General
    Status      : Stable

Code:

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◆ cdna_coding_start()

public Int Bio::EnsEMBL::Exon::cdna_coding_start ( )

    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                  The transcript for which cDNA coordinates should be
                  relative to.
    Example     :

$cdna_coding_start = $exon->cdna_coding_start($transcript);

    Description : Returns the start position of the coding region of the
                  exon in cDNA coordinates.  Returns undef if the whole
                  exon is non-coding.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer or undef
    Exceptions  : Throws if the given argument is not a transcript.
    Caller      : General
    Status      : Stable

Code:

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◆ cdna_end()

public Int Bio::EnsEMBL::Exon::cdna_end ( )

    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                  The transcript for which cDNA coordinates should be
                  relative to.
    Example     :

$cdna_end = $exon->cdna_end($transcript);

    Description : Returns the end position of the exon in cDNA
                  coordinates.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer
    Exceptions  : Throws if the given argument is not a transcript.
                  Throws if the last part of the exon maps into a gap.
                  Throws if the exon can not be mapped at all.
    Caller      : General
    Status      : Stable

Code:

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◆ cdna_start()

public Int Bio::EnsEMBL::Exon::cdna_start ( )

    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                  The transcript for which cDNA coordinates should be
                  relative to.
    Example     :

$cdna_start = $exon->cdna_start($transcript);

    Description : Returns the start position of the exon in cDNA
                  coordinates.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer
    Exceptions  : Throws if the given argument is not a transcript.
                  Throws if the first part of the exon maps into a gap.
                  Throws if the exon can not be mapped at all.
    Caller      : General
    Status      : Stable

Code:

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◆ coding_region_end()

public Int Bio::EnsEMBL::Exon::coding_region_end ( )

    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
    Example     :

$coding_region_end =

$exon->coding_region_end($transcript);

    Description : Returns the end position of the coding region of
                  the exon in slice-relative coordinates on the
                  forward strand.  Returns undef if the whole exon is
                  non-coding.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer or undef
    Exceptions  : Throws if the given argument is not a transcript.
    Caller      : General
    Status      : Stable

Code:

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◆ coding_region_start()

public Int Bio::EnsEMBL::Exon::coding_region_start ( )

    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
    Example     :

$coding_region_start =

$exon->coding_region_start($transcript);

    Description : Returns the start position of the coding region
                  of the exon in slice-relative coordinates on the
                  forward strand.  Returns undef if the whole exon is
                  non-coding.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer or undef
    Exceptions  : Throws if the given argument is not a transcript.
    Caller      : General
    Status      : Stable

Code:

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◆ created_date()

public String Bio::EnsEMBL::Exon::created_date ( )

  Arg [1]    : string $created_date
  Example    :

none

  Description: get/set for attribute created_date
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ display_id()

public String Bio::EnsEMBL::Exon::display_id ( )

  Arg [1]    : none
  Example    :

print $exons->display_id();

  Description: This method returns a string that is considered to be
               the 'display' identifier. For exons this is (depending on
               availability and in this order) the stable Id, the dbID or an
               empty string.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

Code:

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◆ end()

public Int Bio::EnsEMBL::Exon::end ( )

  Arg [1]    : int $end (optional)
  Example    :

$end = $exon->end();

  Description: Getter/Setter for the end of this exon.  The superclass
               implmentation is overridden to flush the internal sequence
               cache if this value is altered
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ end_phase()

public Int Bio::EnsEMBL::Exon::end_phase ( )

  Arg [1]    : (optional) int $end_phase
  Example    :

$end_phase = $feat->end_phase;

  Description: Gets/Sets the end phase of the exon.
               end_phase = number of bases from the last incomplete codon of 
               this exon.
               Usually, end_phase = (phase + exon_length)%3
               but end_phase could be -1 if the exon is half-coding and its 3 
               prime end is UTR.
  Returntype : int
  Exceptions : warning if end_phase is called without an argument and the
               value is not set.
  Caller     : general
  Status     : Stable

Code:

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◆ equals()

public Boolean Bio::EnsEMBL::Exon::equals ( )

  Arg [1]       : Bio::EnsEMBL::Exon exon
  Example       :

if ($exonA->equals($exonB)) { ... }

  Description   : Compares two exons for equality.
                  The test for eqality goes through the following list
                  and terminates at the first true match:

                  1. If Bio::EnsEMBL::Feature::equals() returns false,
                     then the exons are *not* equal.
                  2. If both exons have stable IDs: if these are the
                     same, the exons are equal, otherwise not.
                  3. If the exons have the same start, end, strand, and
                     phase, then they are equal, otherwise not.

  Return type   : Boolean (0, 1)

  Exceptions    : Thrown if a non-transcript is passed as the argument.

Code:

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◆ find_supporting_evidence()

public void Bio::EnsEMBL::Exon::find_supporting_evidence ( )

# This method is only for genebuild backwards compatibility.
# Avoid using it if possible

  Arg [1]    : Bio::EnsEMBL::Feature $features
               The list of features to search for supporting (i.e. overlapping)
               evidence.
  Arg [2]    : (optional) boolean $sorted
               Used to speed up the calculation of overlapping features.  
               Should be set to true if the list of features is sorted in 
               ascending order on their start coordinates.
  Example    :

$exon->find_supporting_evidence(\@features);

  Description: Looks through all the similarity features and
               stores as supporting features any feature
               that overlaps with an exon.  
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Medium Risk

Code:

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◆ flush_supporting_features()

public Bio::EnsEMBL::Exon::flush_supporting_features ( )

  Example     :

$exon->flush_supporting_features;

  Description : Removes all supporting evidence from the exon.
  Return type : (Empty) listref
  Exceptions  : none
  Caller      : general
  Status      : Stable

Code:

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◆ frame()

public Int Bio::EnsEMBL::Exon::frame ( )

  Arg [1]    : none
  Example    :

$frame = $exon->frame

  Description: Gets the frame of this exon
  Returntype : int
  Exceptions : thrown if an arg is passed
               thrown if frame cannot be calculated due to a bad phase value
  Caller     : general
  Status     : Stable

Code:

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◆ get_all_supporting_features()

public Listreference Bio::EnsEMBL::Exon::get_all_supporting_features ( )

  Arg [1]    : none
  Example    :

@evidence = @{$exon->get_all_supporting_features()};

  Description: Retrieves any supporting features added manually by 
               calls to add_supporting_features. If no features have been
               added manually and this exon is in a database (i.e. it has
               an adaptor), fetch from the database
  Returntype : listreference of Bio::EnsEMBL::BaseAlignFeature objects 
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ hashkey()

public String Bio::EnsEMBL::Exon::hashkey ( )

  Arg [1]    : none
  Example    :

if(exists $hash{$exon->hashkey}) { do_something(); }

  Description: Returns a unique hashkey that can be used to uniquely identify
               this exon.  Exons are considered to be identical if they share
               the same seq_region, start, end, strand, phase, end_phase.
               Note that this will consider two exons on different slices
               to be different, even if they actually are not. 
  Returntype : string formatted as slice_name-start-end-strand-phase-end_phase
  Exceptions : thrown if not all the necessary attributes needed to generate
               a unique hash value are set
               set
  Caller     : general
  Status     : Stable

Code:

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◆ is_coding()

public Int Bio::EnsEMBL::Exon::is_coding ( )

  Arg [1]    : Bio::EnsEMBL::Transcript
  Example    :

$exon->is_coding()

  Description: Says if the exon is within the translation or not
  Returntype : Int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ is_constitutive()

public Int Bio::EnsEMBL::Exon::is_constitutive ( )

  Arg [1]    : Boolean $is_constitutive
  Example    :

$exon->is_constitutive(0)

  Description: Getter/setter for is_constitutive state of this exon.
  Returntype : Int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ is_current()

public Int Bio::EnsEMBL::Exon::is_current ( )

  Arg [1]    : Boolean $is_current
  Example    :

$exon->is_current(1)

  Description: Getter/setter for is_current state of this exon.
  Returntype : Int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ load()

public Nothing Bio::EnsEMBL::Exon::load ( )

  Args          : None
  Example       :

$exon->load();

  Description   : The Ensembl API makes extensive use of
                  lazy-loading.  Under some circumstances (e.g.,
                  when copying genes between databases), all data of
                  an object needs to be fully loaded.  This method
                  loads the parts of the object that are usually
                  lazy-loaded.
  Returns       : Nothing.

Code:

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◆ modified_date()

public String Bio::EnsEMBL::Exon::modified_date ( )

  Arg [1]    : string $modified_date
  Example    :

none

  Description: get/set for attribute modified_date
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ move()

public void Bio::EnsEMBL::Exon::move ( )

  Arg [1]    : int start
  Arg [2]    : int end
  Arg [3]    : (optional) int strand
  Example    :

None

  Description: Sets the start, end and strand in one call rather than in 
               3 seperate calls to the start(), end() and strand() methods.
               This is for convenience and for speed when this needs to be
               done within a tight loop.  This overrides the superclass
               move() method so that the internal sequence cache can be
               flushed if the exon if moved.
  Returntype : none
  Exceptions : Thrown is invalid arguments are provided
  Caller     : general
  Status     : Stable

Code:

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◆ new()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::Exon::new ( )

  Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this
                feature is on. The coordinates of the created feature are
                relative to the start of the slice.
  Arg [-START]: The start coordinate of this feature relative to the start
                of the slice it is sitting on.  Coordinates start at 1 and
                are inclusive.
  Arg [-END]  : The end coordinate of this feature relative to the start of
                the slice it is sitting on.  Coordinates start at 1 and are
                inclusive.
  Arg [-STRAND]: The orientation of this feature.  Valid values are 1,-1,0.
  Arg [-SEQNAME] : (optional) A seqname to be used instead of the default name
                of the of the slice.  Useful for features that do not have an
                attached slice such as protein features.
  Arg [-dbID]   : (optional) internal database id
  Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
  Arg [-PHASE]    : the phase. 
  Arg [-END_PHASE]: the end phase
  Arg [-STABLE_ID]: (optional) the stable id of the exon
  Arg [-VERSION]  : (optional) the version
  Arg [-CREATED_DATE] : (optional) the created date
  Arg [-MODIFIED_DATE]: (optional) the last midifeid date

  Example    :

none

  Description: create an Exon object
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : if phase is not valid (i.e. 0,1, 2 -1)
  Caller     : general
  Status     : Stable

Code:

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◆ peptide()

public Bio::Seq Bio::EnsEMBL::Exon::peptide ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $tr
  Example    :

my $pep_str = $exon->peptide($transcript)->seq;

  Description: Retrieves the portion of the transcripts peptide
               encoded by this exon.  The transcript argument is necessary
               because outside of the context of a transcript it is not
               possible to correctly determine the translation.  Note that
               an entire amino acid will be present at the exon boundaries
               even if only a partial codon is present.  Therefore the 
               concatenation of all of the peptides of a transcripts exons 
               is not the same as a transcripts translation because the 
               summation may contain duplicated amino acids at splice sites.
               In the case that this exon is entirely UTR, a Bio::Seq object 
               with an empty sequence string is returned.
  Returntype : Bio::Seq
  Exceptions : thrown if transcript argument is not provided
  Caller     : general
  Status     : Stable

Code:

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◆ phase()

public Int Bio::EnsEMBL::Exon::phase ( )

  Arg [1]    : (optional) int $phase
  Example    :

my $phase = $exon->phase;

$exon->phase(2);

  Description: Gets/Sets the phase of the exon.
  Returntype : int
  Exceptions : throws if phase is not (0, 1 2 or -1).
  Caller     : general
  Status     : Stable

Get or set the phase of the Exon, which tells the
translation machinery, which makes a peptide from
the DNA, where to start.

The Ensembl phase convention can be thought of as
"the number of bases of the first codon which are
on the previous exon".  It is therefore 0, 1 or 2
(or -1 if the exon is non-coding).  In ascii art,
with alternate codons represented by ### and
+++:

       Previous Exon   Intron   This Exon
    ...-------------            -------------...

    5'                    Phase                3'
    ...#+++###+++###          0 +++###+++###+...
    ...+++###+++###+          1 ++###+++###++...
    ...++###+++###++          2 +###+++###+++...

Here is another explanation from Ewan:

Phase means the place where the intron lands
inside the codon - 0 between  codons, 1 between
the 1st and second base, 2 between the second and
3rd  base. Exons therefore have a start phase and
a end phase, but introns have just one phase.

Code:

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◆ rank()

public Int Bio::EnsEMBL::Exon::rank ( )

    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                  The transcript for which the exon rank
                  is requested.
    Example     :

$rank = $exon->rank($transcript);

    Description : Returns the rank of the exon relative to
                  the transcript.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer
    Exceptions  : Throws if the given argument is not a transcript.
                  Throws if the exon does not belong to the transcript.
    Caller      : General
    Status      : Stable

Code:

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◆ seq()

public Bio::Seq Bio::EnsEMBL::Exon::seq ( )

  Arg [1]    : none
  Example    :

my $seq_str = $exon->seq->seq;

  Description: Retrieves the dna sequence of this Exon.
               Returned in a Bio::Seq object.  Note that the sequence may
               include UTRs (or even be entirely UTR).
  Returntype : Bio::Seq or undef
  Exceptions : warning if argument passed,
               warning if exon does not have attatched slice
               warning if exon strand is not defined (or 0)
  Caller     : general
  Status     : Stable

Code:

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sub seq {
  my ( $self, $arg ) = @_;
 
  if ( defined $arg ) {
    warning("seq setting on Exon not supported currently");
    $self->{'_seq_cache'} = $arg->seq();
  }
 
  if ( !defined( $self->{'_seq_cache'} ) ) {
    my $seq;
 
    if ( !defined $self->slice() ) {
      warning("Cannot retrieve seq for exon without slice\n");
      return undef;
    }
 
    if ( !$self->strand() ) {
      warning("Cannot retrieve seq for unstranded exon\n");
      return undef;
    }
 
    if ($self->slice->is_circular() ) {
  if (    $self->slice->start > $self->slice->end) {
# Normally exons overlapping chromosome origin will have negative feature start, but slice will be from 1 .. length 
# But in case you got an exon attached to  a sub slice try this
      my $mid_point = $self->slice()->seq_region_length() - $self->slice()->start() + 1;
      my $seq1 =  $self->slice()->subseq( $self->start(), $mid_point, $self->strand() );
 
      my $seq2 = $self->slice()->subseq( $mid_point + 1, $self->end(), $self->strand() );
 
      $seq = $self->strand() > 0 ? "$seq1$seq2" : "$seq2$seq1";
  } elsif ( $self->start < 0 ||  $self->start > $self->end) {
# Normally exons overlapping chromosome origin will be 0 based, and can have negative start
# But if you go via sub_Slice it gives you chromosome based coordinates, i.e it will have start greater then end
      my $start_point = $self->slice->seq_region_length + $self->slice->start;
      my $mid_point = $self->slice->seq_region_length;
      my $seq1 =  $self->slice->subseq( $self->start, $mid_point, $self->strand);
      my $seq2 = $self->slice->subseq(1, $self->end, $self->strand );
      $seq = $self->strand > 0 ? "$seq1$seq2" : "$seq2$seq1";
  } else {
# End this is the case for genes not overlapping the origin
      $seq = $self->slice()->subseq( $self->start(), $self->end(), $self->strand() );
  }
    } else {
  $seq = $self->slice()->subseq( $self->start(), $self->end(), $self->strand() );
    }
 
    $self->{'_seq_cache'} = $seq;
  } ## end if ( !defined( $self->...))
 
  return
    Bio::Seq->new( -seq      => $self->{'_seq_cache'},
                   -id       => $self->display_id,
                   -moltype  => 'dna',
                   -alphabet => 'dna' );
} ## end sub seq

◆ slice()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Exon::slice ( )

  Arg [1]    : Bio::EnsEMBL::Slice
  Example    :

$slice = $exon->slice();

  Description: Getter/Setter for the slice this exon is on.  The superclass
               implmentation is overridden to flush the internal sequence
               cache if this value is altered
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ stable_id()

public String Bio::EnsEMBL::Exon::stable_id ( )

  Arg [1]    : string $stable_id
  Example    :

none

  Description: get/set for attribute stable_id
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ stable_id_version()

public String Bio::EnsEMBL::Exon::stable_id_version ( )

  Arg [1]    : (optional) String - the stable ID with version to set
  Example    :

$exon->stable_id("ENSE0000000001.3");

  Description: Getter/setter for stable id with version for this exon.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ start()

public Int Bio::EnsEMBL::Exon::start ( )

  Arg [1]    : int $start (optional)
  Example    :

$start = $exon->start();

  Description: Getter/Setter for the start of this exon.  The superclass
               implmentation is overridden to flush the internal sequence
               cache if this value is altered
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ strand()

public Int Bio::EnsEMBL::Exon::strand ( )

  Arg [1]    : int $strand (optional)
  Example    :

$start = $exon->strand();

  Description: Getter/Setter for the strand of this exon.  The superclass
               implmentation is overridden to flush the internal sequence
               cache if this value is altered
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ summary_as_hash()

public Hashref Bio::EnsEMBL::Exon::summary_as_hash ( )

  Example       :

$exon_summary = $exon->summary_as_hash();

  Description   : Extends Feature::summary_as_hash
                  Retrieves a summary of this Exon.
  Returns       : hashref of descriptive strings
  Status        : Intended for internal use

Code:

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◆ transfer()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::Exon::transfer ( )

  Arg [1]    : Bio::EnsEMBL::Slice $destination_slice
  Example    :

none

  Description: Moves this Exon to given target slice coordinates. If Features
               are attached they are moved as well. Returns a new exon.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ transform()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::Exon::transform ( )

  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Description: moves this exon to the given coordinate system. If this exon has
               attached supporting evidence, they move as well.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : wrong parameters
  Caller     : general
  Status     : Stable

Code:

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◆ version()

public String Bio::EnsEMBL::Exon::version ( )

  Arg [1]    : string $version
  Example    :

none

  Description: get/set for attribute version
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

ensembl/modules/Bio/EnsEMBL/Exon.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _merge_ajoining_coords()

◆ add_supporting_features()

◆ adjust_start_end()

◆ cdna_coding_end()

◆ cdna_coding_start()

◆ cdna_end()

◆ cdna_start()

◆ coding_region_end()

◆ coding_region_start()

◆ created_date()

◆ display_id()

◆ end()

◆ end_phase()

◆ equals()

◆ find_supporting_evidence()

◆ flush_supporting_features()

◆ frame()

◆ get_all_supporting_features()

◆ hashkey()

◆ is_coding()

◆ is_constitutive()

◆ is_current()

◆ load()

◆ modified_date()

◆ move()

◆ new()

◆ peptide()

◆ phase()

◆ rank()

◆ seq()

◆ slice()

◆ stable_id()

◆ stable_id_version()

◆ start()

◆ strand()

◆ summary_as_hash()

◆ transfer()

◆ transform()

◆ version()