Inheritance diagram for Bio::EnsEMBL::Feature:

Public Member Functions
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

my $feat = new Bio::EnsEMBL::Feature(
  -start  => 100,
  -end    => 220,
  -strand => -1,
  -slice  => $slice,
  -analysis => $analysis
);
 
my $start  = $feat->start();
my $end    = $feat->end();
my $strand = $feat->strand();
 
# Move the feature to the chromosomal coordinate system
$feature = $feature->transform('chromosome');
 
# Move the feature to a different slice (possibly on another coord
# system)
$feature = $feature->transfer($new_slice);
 
# Project the feature onto another coordinate system possibly across
# boundaries:
@projection = @{ $feature->project('contig') };
 
# Change the start, end, and strand of the feature in place
$feature->move( $new_start, $new_end, $new_strand );

Description

This is the Base feature class from which all Ensembl features inherit.
It provides a bare minimum functionality that all features require.  It
basically describes a location on a sequence in an arbitrary coordinate
system.

Definition at line 47 of file Feature.pm.

Member Function Documentation

◆ add_sub_SeqFeature()

public Bio::EnsEMBL::Feature::add_sub_SeqFeature ( )

 Deprecated:

only for genebuild backward compatibility.
 Avoid using it if possible


 
    Code:

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sub add_sub_SeqFeature{
  my ($self,$feat,$expand) = @_;
  my ($p, $f, $l) = caller;
  if( $expand eq 'EXPAND' ) {
    # if this doesn't have start/end set - forget it!
    if( ! $self->start && ! $self->end ) {
      
      $self->start($feat->start());
      $self->end($feat->end());
      $self->strand($feat->strand);
    } else {
      if( $feat->start < $self->start ) {
        $self->start($feat->start);
      }
 
      if( $feat->end > $self->end ) {
        $self->end($feat->end);
      }
    }
   } else {
     if($self->start > $feat->start || $self->end < $feat->end) {
       throw("$feat is not contained within parent feature, " .
             "and expansion is not valid");
     }
   }
 
   push(@{$self->{'_gsf_sub_array'}},$feat);
}

◆ analysis()

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::Feature::analysis ( )

  Arg [1]    : (optional) Bio::EnsEMBL::Analysis $analysis
  Example    :

$feature->analysis(new Bio::EnsEMBL::Analysis(...))

  Description: Getter/Setter for the analysis that is associated with 
               this feature.  The analysis describes how this feature 
               was derived.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : thrown if an invalid argument is passed
  Caller     : general
  Status     : Stable

Code:

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◆ coord_system_name()

public String Bio::EnsEMBL::Feature::coord_system_name ( )

  Arg [1]    : none
  Example    :

print $feature->coord_system_name()

  Description: Gets the name of the coord_system which this feature is on.
               Returns undef if this Feature is not on a slice.
  Returntype : string or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ display_id()

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

  Arg [1]    : none
  Example    :

print $f->display_id();

  Description: This method returns a string that is considered to be
               the 'display' identifier.  It is overridden by subclasses to
               return an appropriate value for objects of that particular 
               class.  If no appropriate display id is available an empty
               string is returned instead.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

Code:

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◆ end()

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

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

$end = $feat->end();

  Description: Getter/Setter for the end of this feature relative to the
               start of the slice that it is on.  Note that negative values,
               of values exceeding the length of the slice are permitted.  End
               must be greater than or equal to start regardless of the strand.
               Coordinate values start at 1 and are inclusive.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ equals()

public Boolean Or Undef Bio::EnsEMBL::Feature::equals ( )

  Arg [1]       : Bio::EnsEMBL::Feature object
  Example       :

if ($featureA->equals($featureB)) { ... }

  Description   : Compares two features using various criteria.  The
                  test for eqality goes through the following list and
                  terminates at the first true match:

                  1. If the two features are the same object, they are
                     equal.
                  2. If they are of different types (e.g., transcript
                     and gene), they are *not* equal.
                  3. If they both have dbIDs: if these are the same,
                     then they are equal, otherwise not.
                  4. If they both have slices and analysis objects:
                     if the analysis dbIDs are the same and the
                     seq_region_id are the same, along with
                     seq_region_start and seq_region_end, then they are
                     equal, otherwise not.

                  If none of the above is able to determine equality,
                  undef is returned.

    Return type : tri-Boolean (0, 1, undef = "unknown")

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

Code:

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◆ feature_Slice()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Feature::feature_Slice ( )

  Args       : none
  Example    :

$slice = $feature->feature_Slice()

  Description: This is a convenience method to return a slice that covers the
               Area of this feature. The feature start will be at 1 on it, and
               it will have the length of this feature.
  Returntype : Bio::EnsEMBL::Slice or undef if this feature has no attached
               Slice.
  Exceptions : warning if Feature does not have attached slice.
  Caller     : web drawing code
  Status     : Stable

Code:

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◆ feature_so_acc()

public String Bio::EnsEMBL::Feature::feature_so_acc ( )

  Description: This method returns a string containing the SO accession number of the feature
               Define constant SEQUENCE_ONTOLOGY in classes that require it, or override it for multiple possible values for a class.
  Returntype : String (Sequence Ontology accession number)
  Exceptions : Thrown if caller SEQUENCE_ONTOLOGY is undefined and is not a Bio::EnsEMBL::Feature

Code:

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◆ feature_so_term()

public String Bio::EnsEMBL::Feature::feature_so_term ( )

  Description: This method returns a string containing the SO term of the feature
               Define constant SEQUENCE_ONTOLOGY in classes that require it, or override it for multiple possible values for a class.
  Returntype : String (Sequence Ontology term)
  Exceptions : Thrown if caller SEQUENCE_ONTOLOGY is undefined and is not a Bio::EnsEMBL::Feature

Code:

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◆ flush_sub_SeqFeature()

public Bio::EnsEMBL::Feature::flush_sub_SeqFeature ( )

 Deprecated:

Only for genebuild backwards compatibility.
 Avoid using it if possible


 
    Code:

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sub flush_sub_SeqFeature {
  my ($self) = @_;
  $self->{'_gsf_sub_array'} = [];
}

◆ get_all_alt_locations()

public Listref Bio::EnsEMBL::Feature::get_all_alt_locations ( )

  Arg [1]    : Boolean override flag to force the method to return all 
               Features on the reference sequence as well.

  Example    :

@features = @{$feature->get_all_alt_locations()};
              foreach $f (@features) {
                print $f->slice->seq_region_name,' ',$f->start, $f->end,"\n";
              }

  Description: Retrieves shallow copies of this feature in its alternate
               locations.  A feature can be considered to have multiple
               locations when it sits on a alternative structural haplotype
               or when it is on a Pseudo Autosomal Region.  Most features will
               just return a reference to an empty list though.
               The features returned by this method will be on a slice which
               covers the entire alternate region.

               Currently this method does not take into account alternate
               locations on the alternate locations (e.g. a reference
               sequence may have multiple alternate haplotypes.  Asking
               for alternate locations of a feature on one of the alternate
               haplotypes will give you back the reference location, but not
               locations on the other alternate haplotypes).

  Returntype : listref of features of the same type of this feature.
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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sub get_all_alt_locations {
  my $self = shift;
  my $return_all = shift || 0;
 
  my $slice = $self->{'slice'} or return [];
  my $sa = $slice->adaptor() or return [];
 
  # get slice of entire region
  $slice = $sa->fetch_by_seq_region_id($slice->get_seq_region_id);
 
  my $axfa = $sa->db->get_AssemblyExceptionFeatureAdaptor();
  my $axfs = $axfa->fetch_all_by_Slice($slice);
 
  my (@haps, @alt);
 
  foreach my $axf (@$axfs) {
    if(uc($axf->type()) eq 'HAP') {
      push @haps, $axf;
    } elsif(uc($axf->type()) =~ 'PAR') {
      push @alt, $axf;
    } elsif( $axf->type() eq "PATCH_FIX"){
      push @haps, $axf;
    } elsif( $axf->type() eq "PATCH_FIX REF"){
      push @haps, $axf  if $return_all > 0 ;
    } elsif( $axf->type() eq "HAP REF" ) {
      push @haps, $axf if $return_all > 0 ;
      # do nothing when you are on REF
    } elsif( $axf->type() eq "PATCH_NOVEL"){
      push @haps, $axf;
    }elsif( $axf->type() eq "PATCH_NOVEL REF"){
      push @haps, $axf  if $return_all > 0 ;
    } else {
      warning("Unknown exception feature type ". $axf->type()."- ignoring.");
    }
  }
 
  # regions surrounding hap are those of interest, not hap itself
  # convert hap alt. exc. features to regions around haps instead
  foreach my $h (@haps) {
    my $haslice = $h->alternate_slice();
    my $hacs    = $haslice->coord_system();
 
    if($h->start() > 1 && $haslice->start() > 1) {
      my $aslice = $sa->fetch_by_region($hacs->name(),
                                        $haslice->seq_region_name(),
                                        1,
                                        $haslice->start()-1,
                                        $haslice->strand(),
                                        $hacs->version());
 
      push @alt, Bio::EnsEMBL::AssemblyExceptionFeature->new
        (-start  => 1,
         -end    => $h->start()-1,
         -alternate_slice => $aslice);
    }
 
    if($h->end() < $slice->seq_region_length() &&
       $haslice->end < $haslice->seq_region_length()) {
      my $aslice = $sa->fetch_by_region($hacs->name(),
                                        $haslice->seq_region_name(),
                                        $haslice->end()+1,
                                        $haslice->seq_region_length(),
                                        $haslice->strand(),
                                        $hacs->version());
 
      push @alt, Bio::EnsEMBL::AssemblyExceptionFeature->new
        (-start  => $h->end() + 1,
         -end    => $slice->seq_region_length(),
         -alternate_slice => $aslice);
    }
  }
 
 
  # check if exception regions contain our feature
 
  my @features;
 
  foreach my $axf (@alt) {
    # ignore other region if feature is not entirely on it
    next if($self->seq_region_start() < $axf->start() ||
            $self->seq_region_end()   > $axf->end());
 
    # quick shallow copy of the feature
    my $f;
    %$f = %$self;
    bless $f, ref($self);
 
    my $aslice = $axf->alternate_slice();
 
    # position feature on entire slice of other region
    
    # Cache seq_region_* to prevent contamination when changing feature coordinates.
    my $seq_region_start = $f->seq_region_start();
    my $seq_region_end = $f->seq_region_end();
    
    $f->{'start'}  = $seq_region_start - $axf->start() + $aslice->start();
    $f->{'end'}    = $seq_region_end   - $axf->start() + $aslice->start();
    $f->{'strand'} *= $aslice->strand();
 
    $f->{'slice'} = $sa->fetch_by_seq_region_id($aslice->get_seq_region_id());
 
    push @features, $f;
  }
 
  return \@features;
}

◆ get_nearest_Gene()

public Bio::EnsEMBL::Gene Bio::EnsEMBL::Feature::get_nearest_Gene ( )

  Description: Get the nearest genes to the feature
  Returntype : Bio::EnsEMBL::Gene or undef if none can be found nearby
  Caller     : general
  Status     : At risk

Code:

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◆ get_overlapping_Genes()

public List Bio::EnsEMBL::Feature::get_overlapping_Genes ( )

  Arg [1]    : Optional Boolean: Stranded match i.e. match strand of Feature and Genes
  Arg [2]    : Optional Boolean: Get Genes with an overlapping 5' end
  Arg [3]    : Optional Boolean: Get Genes with an overlapping 3' end
  Description: Get all the genes that overlap this feature.
  Returntype : list ref of Bio::EnsEMBL::Gene
  Caller     : general
  Status     : UnStable

Code:

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◆ length()

public Int Bio::EnsEMBL::Feature::length ( )

  Arg [1]    : none
  Example    :

$length = $feat->length();

  Description: Returns the length of this feature
  Returntype : Integer
  Exceptions : Throws if end < start and the feature is not on a
               circular slice
  Caller     : general
  Status     : Stable

Code:

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◆ move()

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

  Arg [1]    : int start
  Arg [2]    : int end
  Arg [3]    : (optional) int strand
  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.
  Returntype : none
  Exceptions : Thrown is invalid arguments are provided
  Caller     : general
  Status     : Stable

Code:

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◆ new()

public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::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] : 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
  Example    :

$feature = Bio::EnsEMBL::Feature->new(-start    => 1, 
                                                    -end      => 100,
                                                    -strand   => 1,
                                                    -slice    => $slice,
                                                    -analysis => $analysis);

  Description: Constructs a new Bio::EnsEMBL::Feature.  Generally subclasses
               of this method are instantiated, rather than this class itself.
  Returntype : Bio::EnsEMBL::Feature
  Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND ,-ADAPTOR arguments
  Caller     : general, subclass constructors
  Status     : Stable

Code:

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◆ overlaps()

public Boolean Bio::EnsEMBL::Feature::overlaps ( )

  Arg [1]    : Bio::EnsEMBL::Feature $f
               The other feature you want to check overlap with this feature
               for.
  Description: This method does a range comparison of this feature's seq_region_start and
               seq_region_end and compares it with another feature's seq_region_start
               and seq_region_end. It will return true if these ranges overlap 
               and the features are on the same seq_region.

               For local coordinate overlaps tests (those values returned from
               start and end) use overlaps_local().
  Returntype : TRUE if features overlap, FALSE if they don't
  Exceptions : warning if features are on different seq_regions
  Caller     : general
  Status     : Stable

Code:

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◆ overlaps_local()

public Boolean Bio::EnsEMBL::Feature::overlaps_local ( )

  Arg [1]    : Bio::EnsEMBL::Feature $f
               The other feature you want to check overlap with this feature
               for.
  Description: This method does a range comparison of this feature's start and
               end and compares it with another feature's start and end. It 
               will return true if these ranges overlap and the features are 
               on the same seq_region.

               This method will not attempt to resolve starts and ends with 
               reference to the feature's backing Slice.

               For global coordinate overlaps tests (with reference to the feature's 
               backing sequence region) use overlaps().
  Returntype : TRUE if features overlap, FALSE if they don't
  Exceptions : warning if features are on different seq_regions
  Caller     : general
  Status     : Stable

Code:

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◆ project()

public Listref Bio::EnsEMBL::Feature::project ( )

  Arg [1]    : string $name
               The name of the coordinate system to project this feature onto
  Arg [2]    : string $version (optional)
               The version of the coordinate system (such as 'NCBI34') to
               project this feature onto
  Example    :

my $clone_projection = $feature->project('clone');
 
foreach my $seg (@$clone_projection) {
  my $clone = $seg->to_Slice();
  print "Features current coords ", $seg->from_start, '-',
    $seg->from_end, " project onto clone coords " .
    $clone->seq_region_name, ':', $clone->start, '-', $clone->end,
    $clone->strand, "\n";
}

  Description: Returns the results of 'projecting' this feature onto another
               coordinate system.  This is useful to see where a feature
               would lie in a coordinate system in which it
               crosses a boundary.

               This method returns a reference to a list of
               Bio::EnsEMBL::ProjectionSegment objects.
               ProjectionSegments are blessed arrays and can also be used as
               triplets [from_start,from_end,to_Slice]. The from_start and
               from_end are the coordinates relative to the feature start.
               For example, if a feature is current 100-200bp on a slice
               then the triplets returned might be:
               [1,50,$slice1],
               [51,101,$slice2]

               The to_Slice is a slice spanning the region on the requested
               coordinate system that this feature projected to.

               If the feature projects entirely into a gap then a reference to
               an empty list is returned.

  Returntype : listref of Bio::EnsEMBL::ProjectionSegments
               which can also be used as [$start,$end,$slice] triplets
  Exceptions : slice does not have an adaptor
  Caller     : general
  Status     : Stable

Code:

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◆ project_to_slice()

public Listref Bio::EnsEMBL::Feature::project_to_slice ( )

  Arg [1]    : slice to project to

  Example    :

my $clone_projection = $feature->project_to_slice($slice);
 
foreach my $seg (@$clone_projection) {
  my $clone = $seg->to_Slice();
  print "Features current coords ", $seg->from_start, '-',
    $seg->from_end, " project onto clone coords " .
    $clone->seq_region_name, ':', $clone->start, '-', $clone->end,
    $clone->strand, "\n";
}

  Description: Returns the results of 'projecting' this feature onto another
               slice . This is useful to see where a feature
               would lie in a coordinate system in which it
               crosses a boundary.

               This method returns a reference to a list of
               Bio::EnsEMBL::ProjectionSegment objects.
               ProjectionSegments are blessed arrays and can also be used as
               triplets [from_start,from_end,to_Slice]. The from_start and
               from_end are the coordinates relative to the feature start.
               For example, if a feature is current 100-200bp on a slice
               then the triplets returned might be:
               [1,50,$slice1],
               [51,101,$slice2]

               The to_Slice is a slice spanning the region on the requested
               coordinate system that this feature projected to.

               If the feature projects entirely into a gap then a reference to
               an empty list is returned.

  Returntype : listref of Bio::EnsEMBL::ProjectionSegments
               which can also be used as [$start,$end,$slice] triplets
  Exceptions : slice does not have an adaptor
  Caller     : general
  Status     : At Risk

Code:

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◆ seq()

public String Bio::EnsEMBL::Feature::seq ( )

  Args       : none
  Example    :

my $dna_sequence = $simple_feature->seq();

  Description: Returns the dna sequence from the attached slice and 
               attached database that overlaps with this feature.
               Returns undef if there is no slice or no database.
               Returns undef if this feature is unstranded (i.e. strand=0).
  Returntype : String or undef
  Exceptions : warning if this feature is not stranded
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_end()

public Int Bio::EnsEMBL::Feature::seq_region_end ( )

  Arg [1]    : none
  Example    :

print $feature->seq_region_end();

  Description: Convenience method which returns the absolute end of this
               feature on the seq_region, as opposed to the relative (slice)
               position.

               Returns undef if this feature is not on a slice or slice is
               circular and cannot determine the position of the feature from
               the db.
  Returntype : int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_length()

public Int Bio::EnsEMBL::Feature::seq_region_length ( )

  Arg [1]    : none
  Example    :

print $feature->seq_region_length();

  Description: Returns the length of the seq_region which this feature is on 
               Returns undef if this Feature is not on a slice.
  Returntype : int (unsigned) or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_name()

public String Bio::EnsEMBL::Feature::seq_region_name ( )

  Arg [1]    : none
  Example    :

print $feature->seq_region_name();

  Description: Gets the name of the seq_region which this feature is on.
               Returns undef if this Feature is not on a slice.
  Returntype : string or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_start()

public Int Bio::EnsEMBL::Feature::seq_region_start ( )

  Arg [1]    : none
  Example    :

print $feature->seq_region_start();

  Description: Convenience method which returns the absolute start of this
               feature on the seq_region, as opposed to the relative (slice) 
               position.

               Returns undef if this feature is not on a slice or slice is
               circular and cannot determine the position of the feature from
               the db.
  Returntype : int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ seq_region_strand()

public Boolean Bio::EnsEMBL::Feature::seq_region_strand ( )

  Arg [1]    : none
  Example    :

print $feature->seq_region_strand();

  Description: Returns the strand of the seq_region which this feature is on 
               (i.e. feature_strand * slice_strand)
               Returns undef if this Feature is not on a slice.
  Returntype : 1,0,-1 or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ seqname()

public String Bio::EnsEMBL::Feature::seqname ( )

  Arg [1]    : (optional) $seqname
  Example    :

$seqname = $feat->seqname();

  Description: Getter/Setter for the name of the sequence that this feature
               is on. Normally you can get away with not setting this value
               and it will default to the name of the slice on which this
               feature is on.  It is useful to set this value on features which
               do not ordinarily sit on features such as ProteinFeatures which
               sit on peptides.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ slice()

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

  Arg [1]    : (optional) Bio::EnsEMBL::Slice $slice
  Example    :

$seqname = $feature->slice()->name();

  Description: Getter/Setter for the Slice that is associated with this 
               feature.  The slice represents the underlying sequence that this
               feature is on.  Note that this method call is analagous to the
               old SeqFeature methods contig(), entire_seq(), attach_seq(),
               etc.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : thrown if an invalid argument is passed
  Caller     : general
  Status     : Stable

Code:

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◆ species()

public String Bio::EnsEMBL::Feature::species ( )

  Example     :

$feature->species();

  Description : Shortcut to the feature's DBAdaptor and returns its species name 
  Returntype  : String the species name
  Exceptions  : Thrown if there is no attached adaptor
  Caller      : Webcode

Code:

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◆ start()

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

  Arg [1]    : (optional) int $start
               The start of this feature relative to the start of the slice
               that it is on.
  Example    :

$start = $feat->start()

  Description: Getter/Setter for the start of this feature relative to the 
               start of the slice it is on.  Note that negative values, or
               values exceeding the length of the slice are permitted.
               Start must be less than or equal to the end regardless of the 
               strand. Coordinate values start at 1 and are inclusive.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ strand()

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

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

$feat->strand(-1);

  Description: Getter/Setter for the strand of this feature relative to the
               slice it is on.  0 is an unknown or non-applicable strand.  
               -1 is the reverse (negative) strand and 1 is the forward 
               (positive) strand.  No other values are permitted.
  Returntype : int
  Exceptions : thrown if an invalid strand argument is passed
  Caller     : general
  Status     : Stable

Code:

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◆ sub_SeqFeature()

public Bio::EnsEMBL::Feature::sub_SeqFeature ( )

 Deprecated:

For genebuild backwards compatibility.
 Avoid using it if possible


 
    Code:

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sub sub_SeqFeature{
  my ($self) = @_;
  return @{$self->{'_gsf_sub_array'}} if($self->{'_gsf_sub_array'});
}

◆ summary_as_hash()

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

  Example       :

$feature_summary = $feature->summary_as_hash();

  Description   : Retrieves a textual summary of this Feature.
                  Should be overidden by subclasses for specific tweaking
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use

Code:

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◆ transfer()

public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::transfer ( )

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice to transfer this feature to
  Example    :

$feature = $feature->transfer($slice);

next if(!defined($feature));

  Description: Returns a copy of this feature which has been shifted onto
               another slice.

               If the new slice is in a different coordinate system the
               feature is transformed first and then placed on the slice.
               If the feature would be split across a coordinate system
               boundary or mapped to a gap undef is returned instead.

               If the feature cannot be placed on the provided slice because
               it maps to an entirely different location, undef is returned
               instead.

  Returntype : Bio::EnsEMBL::Feature (or undef)
  Exceptions : throw on incorrect argument
               throw if feature does not have attached slice
  Caller     : general, transform()
  Status     : Stable

Code:

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sub transfer {
  my $self = shift;
  my $slice = shift;
 
  if(!$slice || !ref($slice) || (!$slice->isa('Bio::EnsEMBL::Slice') && !$slice->isa('Bio::EnsEMBL::LRGSlice'))) {
    throw('Slice argument is required');
  }
 
  #make a shallow copy of the feature to be transfered
  my $feature;
  %{$feature} = %{$self};
  bless $feature, ref($self);
  weaken $feature->{adaptor};
 
  my $current_slice = $self->{'slice'};
 
  if(!$current_slice) {
    warning("Feature cannot be transfered without attached slice.");
    return undef;
  }
 
  my $cur_cs = $current_slice->coord_system();
  my $dest_cs = $slice->coord_system();
 
  #if we are not in the same coord system a transformation step is needed first
  if(!$dest_cs->equals($cur_cs)) {
    $feature = $feature->transform($dest_cs->name, $dest_cs->version, $slice);
    return undef if(!defined($feature));
    $current_slice = $feature->{'slice'};
  }
 
  # feature went to entirely different seq_region
  if($current_slice->seq_region_name() ne $slice->seq_region_name()) {
    return undef;
  }
 
  #if the current feature positions are not relative to the start of the
  #seq region, convert them so they are
  my $cur_slice_start  = $current_slice->start();
  my $cur_slice_strand = $current_slice->strand();
  if($cur_slice_start != 1 || $cur_slice_strand != 1) {
    my $fstart = $feature->{'start'};
    my $fend   = $feature->{'end'};
 
    if($cur_slice_strand == 1) {
      $feature->{'start'} = $fstart + $cur_slice_start - 1;
      $feature->{'end'}   = $fend   + $cur_slice_start - 1;
    } else {
      my $cur_slice_end = $current_slice->end();
      $feature->{'start'}  = $cur_slice_end - $fend   + 1;
      $feature->{'end'}    = $cur_slice_end - $fstart + 1;
      $feature->{'strand'} *= -1;
    }
  }
 
  my $fstart = $feature->{'start'};
  my $fend   = $feature->{'end'};
 
  #convert to destination slice coords
  if($slice->strand == 1) {
    $feature->{'start'} = $fstart - $slice->start() + 1;
    $feature->{'end'}   = $fend   - $slice->start() + 1;
  } else {
    $feature->{'start'} = $slice->end() - $fend   + 1;
    $feature->{'end'}   = $slice->end() - $fstart + 1;
    $feature->{'strand'} *= -1;
  }
 
  $feature->{'slice'} = $slice;
 
  return $feature;
}

◆ transform()

public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::transform ( )

  Arg [1]    : string $coord_system
               The coord system to transform this feature to.
  Arg [2]    : string $version (optional)
               The version of the coord system to transform this feature to.
  Arg [3]    : Bio::EnsEMBL::Slice (optional)
               Specified when a projection may land on many overlapping slices
               and disambiguation is required.
  Example    :

$feature = $feature->transform('contig');

next if(!defined($feature));

  Description: Returns a copy of this feature, but converted to a different
               coordinate system. The converted feature will be placed on a
               slice which spans an entire sequence region of the new
               coordinate system. If the requested coordinate system is the
               same coordinate system it is simply placed on a slice which
               spans the entire seq_region (as opposed to the original slice
               which may have only partially covered the seq_region).

               If a feature spans a boundary in the new coordinate system,
               undef is returned instead.

               For example, transforming an exon in contig coordinates to one 
               in chromosomal coodinates will place the exon on a slice of an 
               entire chromosome.
  Returntype : Bio::EnsEMBL::Feature (or undef)
  Exceptions : thrown if an invalid coordinate system is provided
               warning if Feature is not attached to a slice
  Caller     : general, transfer()
  Status     : Stable

Code:

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sub transform {
  my $self = shift;
  my $cs_name = shift;
  my $cs_version = shift;
  my $to_slice = shift;
 
  my $slice = $self->{'slice'};
 
  if(!$slice) {
    warning("Feature cannot be transformed without attached slice.");
    return undef;
  }
 
  if(!$slice->adaptor()) {
    warning("Feature cannot be transformed without adaptor on" .
            " attached slice.");
    return undef;
  }
 
  #use db from slice since this feature may not yet be stored in a database
  my $db = $slice->adaptor->db();
  my $cs = $db->get_CoordSystemAdaptor->fetch_by_name($cs_name, $cs_version);
  my $current_cs = $slice->coord_system();
 
  if(!$current_cs) {
    warning("Feature cannot be transformed without CoordSystem on " .
            "attached slice.");
    return undef;
  }
 
  if(!$cs) {
    throw("Cannot transform to unknown coordinate system " .
          "[$cs_name $cs_version]\n");
  }
 
  # if feature is already in the requested coordinate system, we can just
  # return a copy
  if( $cs->equals( $current_cs ) && $slice->start() == 1 &&
      $slice->strand() == 1 ) {
    my $new_feature;
    %$new_feature = %$self;
    bless $new_feature, ref $self;
    return $new_feature;
  }
  my $projection;
  if(defined($to_slice)){
    $projection = $self->project_to_slice( $to_slice );  }
  else{
    $projection = $self->project( $cs_name, $cs_version );
  }
 
  if(@$projection == 0){
    return undef;
  }
  if( @$projection != 1 and !defined($to_slice)) {
#    warn "MORE than one projection and NO slice specified ";
#    warn "from ".$self->slice->name." to $cs_name, $cs_version\n";
    return undef;
  }
  my $index = 0;
  if(defined($to_slice)){
    my $found = 0;
    my $i = 0;
    foreach my $proj (@{$projection}) {
      my $slice = $proj->[2];
      if($to_slice->get_seq_region_id eq $slice->get_seq_region_id){
    $found =1;
    $index = $i;
      }
      $i++;
    }
    if(!$found){
      if(@$projection != 1){
    if(@$projection == 0){
      warn "number of mappings is ".@$projection."\n";
      warn "could not project feature ".ref($self)." from ".$self->slice->seq_region_name." to ".$to_slice->seq_region_name."\n";
      warn "In the region of ".$self->slice->start." <-> ".$self->slice->end."\n";
      warn "feat start=".($self->slice->start+$self->start)."\tend=".($self->slice->start+$self->end)."\n";
    }
    else{
      foreach my $proj (@{$projection}) {
        my $slice = $proj->[2];
        warn "available slice ".$slice->seq_region_name."\n";
      }
      warn "MORE than one projection and no to slice specified (".$to_slice->seq_region_name.")\n";
    }
      } 
      else {
    foreach my $proj (@{$projection}) {
      warn "Mapping is to ".$proj->[2]->seq_region_name."\n";
    }
    warn "One projection but none to slice specified\n";
      }
      return undef;
    }
  }
 
  my $p_slice = $projection->[$index]->[2];
  my $slice_adaptor = $db->get_SliceAdaptor;
  $slice = $slice_adaptor->fetch_by_region($p_slice->coord_system()->name(),
                       $p_slice->seq_region_name(),
                       undef, #start
                       undef, #end
                       1, #strand
                       $p_slice->coord_system()->version);
  
  my $new_feature;
  %$new_feature = %$self;
  bless $new_feature, ref $self;
  $new_feature->{'start'}  = $p_slice->start();
  $new_feature->{'end'}    = $p_slice->end();
    $new_feature->{'strand'} =
      ($self->{'strand'} == 0) ? 0 : $p_slice->strand();
  $new_feature->{'slice'}  = $slice;
  return $new_feature;
 
}

◆ version()

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

  Arg [1]    : none
  Example    :

print $f->version();

  Description: This method returns a string that is considered to be
               the identifier version.  It is overridden by subclasses to
               return an appropriate value for objects of that particular
               class.  If no appropriate version is available an empty
               string is returned instead.
  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/Feature.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ add_sub_SeqFeature()

◆ analysis()

◆ coord_system_name()

◆ display_id()

◆ end()

◆ equals()

◆ feature_Slice()

◆ feature_so_acc()

◆ feature_so_term()

◆ flush_sub_SeqFeature()

◆ get_all_alt_locations()

◆ get_nearest_Gene()

◆ get_overlapping_Genes()

◆ length()

◆ move()

◆ new()

◆ overlaps()

◆ overlaps_local()

◆ project()

◆ project_to_slice()

◆ seq()

◆ seq_region_end()

◆ seq_region_length()

◆ seq_region_name()

◆ seq_region_start()

◆ seq_region_strand()

◆ seqname()

◆ slice()

◆ species()

◆ start()

◆ strand()

◆ sub_SeqFeature()

◆ summary_as_hash()

◆ transfer()

◆ transform()

◆ version()