Public Member Functions
public	new ()

public Int	start ()

public Int	end ()

public	length ()

public	strand ()

public void	move ()

public Float	score ()

public	frame ()

public A	primary_tag ()

public A	source_tag ()

public	analysis ()

public	validate ()

public	vthrow ()

public	validate_prot_feature ()

public	has_tag ()

public Nothing	add_tag_value ()

public	each_tag_value ()

public An	all_tags ()

public String	seqname ()

public	attach_seq ()

public A	seq ()

public	entire_seq ()

public An	sub_SeqFeature ()

public Nothing	add_sub_SeqFeature ()

public void	flush_sub_SeqFeature ()

public	id ()

public Float	percent_id ()

public Float	p_value ()

public	phase ()

public	end_phase ()

public	gffstring ()

public	external_db ()

public Bio::PrimarySeqI	contig ()

public	is_splittable ()

public	transform ()

protected	_transform_to_Slice ()

protected	_transform_between_Slices ()

protected	_transform_to_RawContig ()

Detailed Description

Description

Do not use this module if you can avoid it. It has been replaced by
Bio::EnsEMBL::Feature.  This module has a long history of usage but has
become very bloated, and quite unweildy.  It was decided to replace
it completely with a smaller, light-weight feature class rather than
attempting to refactor this class, and maintain strict backwards
compatibility.

Part of the complexity of this class was in its extensive
inheritance. As an example the following is a simplified inheritance
heirarchy that was present for Bio::EnsEMBL::DnaAlignFeature:

  Bio::EnsEMBL::DnaAlignFeature
  Bio::EnsEMBL::BaseAlignFeature
  Bio::EnsEMBL::FeaturePair
  Bio::EnsEMBL::SeqFeature
  Bio::SeqFeatureI
  Bio::RangeI
  Bio::Root::RootI

The new Bio::EnsEMBL::Feature class is much shorter, and hopefully much
easier to understand and maintain.

Definition at line 30 of file SeqFeature.pm.

Member Function Documentation

◆ _transform_between_Slices()

protected Bio::EnsEMBL::SeqFeature::_transform_between_Slices ( )

Undocumented method

Code:

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◆ _transform_to_RawContig()

protected Bio::EnsEMBL::SeqFeature::_transform_to_RawContig ( )

Undocumented method

Code:

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sub _transform_to_RawContig {
  my($self) = @_;
 
  #print STDERR "transforming ".$self." to raw contig coords\n";
  $self->throw("can't transform coordinates of $self without a contig defined")
   unless $self->contig;
 
  my $slice = $self->contig;
 
  unless($slice->adaptor) {
    $self->throw("can't transform coordinates of $self without an adaptor " .
         "attached to the feature's slice");
  }
 
  my $dbh = $slice->adaptor->db;
 
  my $mapper = 
    $dbh->get_AssemblyMapperAdaptor->fetch_by_type($slice->assembly_type);
  my $rca = $dbh->get_RawContigAdaptor;
 
  #first convert the features coordinates to assembly coordinates
  my($start, $end, $strand);
  if($slice->strand == 1) {
    $start  = $slice->chr_start + $self->start - 1;
    $end    = $slice->chr_start + $self->end   - 1;
    $strand = $self->strand;
  } else {
    $start = $slice->chr_end - $self->end   + 1;
    $end   = $slice->chr_end - $self->start + 1;
    $strand = $self->strand * -1;
  }
 
  #convert the assembly coordinates to RawContig coordinates
  my @mapped = $mapper->map_coordinates_to_rawcontig(
    $slice->chr_name,
    $start,
    $end,
    $strand
  );
 
  unless (@mapped) {
    $self->throw("couldn't map $self");
    return $self;
  }
 
  if (@mapped == 1) {
 
    if ($mapped[0]->isa("Bio::EnsEMBL::Mapper::Gap")) {
      $self->warn("feature lies on gap\n");
      return;
    }
 
    my $rc = $rca->fetch_by_dbID($mapped[0]->id);
 
    $self->start     ($mapped[0]->start);
    $self->end       ($mapped[0]->end);
    $self->strand    ($mapped[0]->strand);
    $self->seqname   ($mapped[0]->id);
    #print STDERR "setting contig to be ".$mapped[0]->id."\n";
    $self->contig($rca->fetch_by_dbID($mapped[0]->id));
 
    return $self;
  }
  else {
 
    # more than one object returned from mapper
    # possibly more than one RawContig in region
 
    my (@gaps, @coords);
 
    foreach my $m (@mapped) {
 
    if ($m->isa("Bio::EnsEMBL::Mapper::Gap")) {
        push @gaps, $m;
    }
    elsif ($m->isa("Bio::EnsEMBL::Mapper::Coordinate")) {
        push @coords, $m;
    }
    }
 
    # case where only one RawContig maps
    if (@coords == 1) {
 
        $self->start  ($coords[0]->start);
        $self->end    ($coords[0]->end);
        $self->strand ($coords[0]->strand);
        $self->seqname($coords[0]->id);
    #print STDERR "2 setting contig to be ".$coords[0]->id."\n";
        $self->contig ($rca->fetch_by_dbID($coords[0]->id));
 
    $self->warn("Feature [$self] truncated as lies partially on a gap");
        return $self;
    }
 
    unless ($self->is_splittable) {
        $self->warn("Feature spans >1 raw contig - can't split\n");
        return;
    }
 
    my @out;
    my $obj = ref $self;
 
    SPLIT: foreach my $map (@mapped) {
 
      if ($map->isa("Bio::EnsEMBL::Mapper::Gap")) {
    $self->warn("piece of evidence lies on gap\n");
    next SPLIT;
      }
 
      my $feat = $obj->new;
 
      $feat->start  ($map->start);
      $feat->end    ($map->end);
      $feat->strand ($map->strand);
      #print STDERR "3 setting contig to be ".$mapped[0]->id."\n";
      $feat->contig ($rca->fetch_by_dbID($map->id));
      $feat->adaptor($self->adaptor) if $self->adaptor();
      $feat->display_label($self->display_label) if($self->can('display_label'));
      $feat->analysis($self->analysis);
      push @out, $feat;
    }
    
    return @out;
  }
}

◆ _transform_to_Slice()

protected Bio::EnsEMBL::SeqFeature::_transform_to_Slice ( )

Undocumented method

Code:

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◆ add_sub_SeqFeature()

public Nothing Bio::EnsEMBL::SeqFeature::add_sub_SeqFeature ( )

 Title   : add_sub_SeqFeature
 Usage   : $feat->add_sub_SeqFeature($subfeat);
           $feat->add_sub_SeqFeature($subfeat,'EXPAND')
 Function: adds a SeqFeature into the subSeqFeature array.
           with no 'EXPAND' qualifer, subfeat will be tested
           as to whether it lies inside the parent, and throw
           an exception if not.

           If EXPAND is used, the parents start/end/strand will
           be adjusted so that it grows to accommodate the new
           subFeature
 Returns : nothing
 Args    : An object which has the SeqFeatureI interface

Code:

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◆ add_tag_value()

public Nothing Bio::EnsEMBL::SeqFeature::add_tag_value ( )

 Title   : add_tag_value
 Usage   : $self->add_tag_value('note',"this is a note");
 Returns : nothing
 Args    : tag (string) and value (any scalar)

Code:

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◆ all_tags()

public An Bio::EnsEMBL::SeqFeature::all_tags ( )

 Title   : all_tags
 Usage   : @tags = $feat->all_tags()
 Function: gives all tags for this feature
 Returns : an array of strings
 Args    : none

Code:

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◆ analysis()

public Bio::EnsEMBL::SeqFeature::analysis ( )

 Title   : analysis
 Usage   : $sf->analysis();
 Function: Store details of the program/database
           and versions used to create this feature.

 Example :

 Returns :
 Args    :

Code:

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◆ attach_seq()

public Bio::EnsEMBL::SeqFeature::attach_seq ( )

 Title   : attach_seq
 Usage   : $sf->attach_seq($seq)
 Function: Attaches a Bio::PrimarySeqI object to this feature. This
           Bio::PrimarySeqI object is for the *entire* sequence: ie
           from 1 to 10000
 Example :

 Returns :
 Args    :

Code:

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◆ contig()

public Bio::PrimarySeqI Bio::EnsEMBL::SeqFeature::contig ( )

  Arg [1]    : Bio::PrimarySeqI $seq
  Example    :

$seq = $self->contig;

  Description: Accessor to attach/retrieve a sequence to/from a feature
  Returntype : Bio::PrimarySeqI
  Exceptions : none
  Caller     : general

Code:

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◆ each_tag_value()

public Bio::EnsEMBL::SeqFeature::each_tag_value ( )

 Title   : each_tag_value
 Usage   :
 Function:
 Example :

 Returns :
 Args    :

Code:

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◆ end()

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

 Title   : end
 Usage   : $end = $feat->end
           $feat->end($end)
 Function: get/set on the end coordinate of the feature
 Returns : integer
 Args    : none

Code:

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◆ end_phase()

public Bio::EnsEMBL::SeqFeature::end_phase ( )

 Title   : end_phase
 Usage   : $end_phase = $feat->end_phase()
           $feat->end_phase($end_phase)
 Function: returns end_phase based on phase and length of feature
 Returns : [0,1,2]
 Args    : none if get, 0,1 or 2 if set.

Code:

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◆ entire_seq()

public Bio::EnsEMBL::SeqFeature::entire_seq ( )

 Title   : entire_seq
 Usage   : $whole_seq = $sf->entire_seq()
 Function: gives the entire sequence that this seqfeature is attached to
 Example :

 Returns :
 Args    :

Code:

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◆ external_db()

public Bio::EnsEMBL::SeqFeature::external_db ( )

 Title   : external_db
 Usage   : $pid = $feat->external_db()
           $feat->external_db($dbid)
 Function: get/set for an external db accession number (e.g.: Interpro)
 Returns :
 Args    : none if get, the new value if set

Code:

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◆ flush_sub_SeqFeature()

public void Bio::EnsEMBL::SeqFeature::flush_sub_SeqFeature ( )

 Title   : flush_sub_SeqFeature
 Usage   : $sf->flush_sub_SeqFeature
 Function: Removes all sub SeqFeature
           (if you want to remove only a subset, take
            an array of them all, flush them, and add
            back only the guys you want)
 Example :

 Returns : none
 Args    : none

Code:

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◆ frame()

public Bio::EnsEMBL::SeqFeature::frame ( )

 Title   : frame
 Usage   : $frame = $feat->frame()
           $feat->frame($frame)
 Function: get/set on frame information
 Returns : 0,1,2
 Args    : none if get, the new value if set

Code:

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◆ gffstring()

public Bio::EnsEMBL::SeqFeature::gffstring ( )

Undocumented method

Code:

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◆ has_tag()

public Bio::EnsEMBL::SeqFeature::has_tag ( )

 Title   : has_tag
 Usage   : $value = $self->has_tag('some_tag')
 Function: Returns the value of the tag (undef if
           none)
 Returns :
 Args    :

Code:

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◆ id()

public Bio::EnsEMBL::SeqFeature::id ( )

Undocumented method

Code:

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◆ is_splittable()

public Bio::EnsEMBL::SeqFeature::is_splittable ( )

Undocumented method

Code:

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◆ length()

public Bio::EnsEMBL::SeqFeature::length ( )

 Title   : length
 Usage   :
 Function:
 Example :

 Returns :
 Args    :

Code:

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◆ move()

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

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

$feature->move(100, 200, -1);

  Description: Moves a feature to a different location.  This is faster
               then calling 3 seperate accesors in a large loop.
  Returntype : none
  Exceptions : none
  Caller     : BaseFeatureAdaptor

Code:

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◆ new()

public Bio::EnsEMBL::SeqFeature::new ( )

Undocumented method

Code:

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◆ p_value()

public Float Bio::EnsEMBL::SeqFeature::p_value ( )

 Title   : p_value
 Usage   : $p_val = $feat->p_value()
           $feat->p_value($p_val)
 Function: get/set on p value information
 Returns : float
 Args    : none if get, the new value if set

Code:

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◆ percent_id()

public Float Bio::EnsEMBL::SeqFeature::percent_id ( )

 Title   : percent_id
 Usage   : $pid = $feat->percent_id()
           $feat->percent_id($pid)
 Function: get/set on percentage identity information
 Returns : float
 Args    : none if get, the new value if set

Code:

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◆ phase()

public Bio::EnsEMBL::SeqFeature::phase ( )

 Title   : phase
 Usage   : $phase = $feat->phase()
           $feat->phase($phase)
 Function: get/set on start phase of predicted exon feature
 Returns : [0,1,2]
 Args    : none if get, 0,1 or 2 if set.

Code:

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◆ primary_tag()

public A Bio::EnsEMBL::SeqFeature::primary_tag ( )

 Title   : primary_tag
 Usage   : $tag = $feat->primary_tag()
           $feat->primary_tag('exon')
 Function: get/set on the primary tag for a feature,
           eg 'exon'
 Returns : a string
 Args    : none

Code:

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◆ score()

public Float Bio::EnsEMBL::SeqFeature::score ( )

 Title   : score
 Usage   : $score = $feat->score()
           $feat->score($score)
 Function: get/set on score information
 Returns : float
 Args    : none if get, the new value if set

Code:

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◆ seq()

public A Bio::EnsEMBL::SeqFeature::seq ( )

 Example :

$tseq = $sf->seq()

 Function: returns the sequence (if any ) for this feature truncated to the range spanning the feature
 Returns : a Bio::PrimarySeq object (I reckon)

Code:

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◆ seqname()

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

  Arg [1]    : string $seqname
  Example    :

$seqname = $self->seqname();

  Description: Obtains the seqname of this features sequence.  This is set
               automatically when a sequence with a name is attached, or may
               be set manually.
  Returntype : string
  Exceptions : none
  Caller     : general, attach_seq

Code:

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◆ source_tag()

public A Bio::EnsEMBL::SeqFeature::source_tag ( )

 Title   : source_tag
 Usage   : $tag = $feat->source_tag()
           $feat->source_tag('genscan');
 Function: Returns the source tag for a feature,
           eg, 'genscan'
 Returns : a string
 Args    : none

Code:

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◆ start()

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

 Title   : start
 Usage   : $start = $feat->start
           $feat->start(20)
 Function: Get/set on the start coordinate of the feature
 Returns : integer
 Args    : none

Code:

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◆ strand()

public Bio::EnsEMBL::SeqFeature::strand ( )

 Title   : strand
 Usage   : $strand = $feat->strand()
           $feat->strand($strand)
 Function: get/set on strand information, being 1,-1 or 0
 Returns : -1,1 or 0
 Args    : none

Code:

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◆ sub_SeqFeature()

public An Bio::EnsEMBL::SeqFeature::sub_SeqFeature ( )

 Title   : sub_SeqFeature
 Usage   : @feats = $feat->sub_SeqFeature();
 Function: Returns an array of sub Sequence Features
 Returns : An array
 Args    : none

Code:

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◆ transform()

public Bio::EnsEMBL::SeqFeature::transform ( )

Undocumented method

Code:

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◆ validate()

public Bio::EnsEMBL::SeqFeature::validate ( )

 Title   : validate
 Usage   : $sf->validate;
 Function: Checks whether all the data is present in the
           object.
 Example :

 Returns :
 Args    :

Code:

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◆ validate_prot_feature()

public Bio::EnsEMBL::SeqFeature::validate_prot_feature ( )

 Title   : validate_prot_feature
 Usage   :
 Function:
 Example :

 Returns :
 Args    :

Code:

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◆ vthrow()

public Bio::EnsEMBL::SeqFeature::vthrow ( )

Undocumented method

Code:

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

ensembl/modules/Bio/EnsEMBL/SeqFeature.pm

Public Member Functions

Detailed Description

Description

Member Function Documentation

◆ _transform_between_Slices()

◆ _transform_to_RawContig()

◆ _transform_to_Slice()

◆ add_sub_SeqFeature()

◆ add_tag_value()

◆ all_tags()

◆ analysis()

◆ attach_seq()

◆ contig()

◆ each_tag_value()

◆ end()

◆ end_phase()

◆ entire_seq()

◆ external_db()

◆ flush_sub_SeqFeature()

◆ frame()

◆ gffstring()

◆ has_tag()

◆ id()

◆ is_splittable()

◆ length()

◆ move()

◆ new()

◆ p_value()

◆ percent_id()

◆ phase()

◆ primary_tag()

◆ score()

◆ seq()

◆ seqname()

◆ source_tag()

◆ start()

◆ strand()

◆ sub_SeqFeature()

◆ transform()

◆ validate()

◆ validate_prot_feature()

◆ vthrow()