Bio::SeqFeature Generic
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Summary
Bio::SeqFeature::Generic - Generic SeqFeature
Package variables
No package variables defined.
Included modules
Bio::Annotation::Collection
Bio::Location::Simple
Bio::Location::Split
Bio::Tools::GFF
Inherit
Bio::AnnotatableI Bio::FeatureHolderI Bio::Root::Root Bio::SeqFeatureI
Synopsis
   $feat = Bio::SeqFeature::Generic->new( 
-start => 10,
-end => 100,
-strand => -1,
-primary => 'repeat', # -primary_tag is a synonym
-source_tag => 'repeatmasker',
-display_name => 'alu family',
-score => 1000,
-tag => { new => 1,
author => 'someone',
sillytag => 'this is silly!' } );
$feat = Bio::SeqFeature::Generic->new( -gff_string => $string ); # if you want explicitly GFF1 $feat = Bio::SeqFeature::Generic->new( -gff1_string => $string ); # add it to an annotated sequence $annseq->add_SeqFeature($feat);
Description
Bio::SeqFeature::Generic is a generic implementation for the
Bio::SeqFeatureI interface, providing a simple object to provide all
the information for a feature on a sequence.
For many Features, this is all you will need to use (for example, this
is fine for Repeats in DNA sequence or Domains in protein
sequence). For other features, which have more structure, this is a
good base class to extend using inheritence to have new things: this
is what is done in the Bio::SeqFeature::Gene,
Bio::SeqFeature::Transcript and Bio::SeqFeature::Exon, which provide
well coordinated classes to represent genes on DNA sequence (for
example, you can get the protein sequence out from a transcript
class).
For many Features, you want to add some piece of information, for
example a common one is that this feature is 'new' whereas other
features are 'old'. The tag system, which here is implemented using a
hash can be used here. You can use the tag system to extend the
Bio::SeqFeature::Generic programmatically: that is, you know that you have
read in more information into the tag 'mytag' which you can then
retrieve. This means you do not need to know how to write inherited
Perl to provide more complex information on a feature, and/or, if you
do know but you do not want to write a new class every time you need
some extra piece of information, you can use the tag system to easily
store and then retrieve information.
The tag system can be written in/out of GFF format, and also into EMBL
format via the Bio::SeqIO system
Methods
new
No description
Code
set_attributesDescriptionCode
direct_newDescriptionCode
locationDescriptionCode
startDescriptionCode
endDescriptionCode
lengthDescriptionCode
strandDescriptionCode
scoreDescriptionCode
frameDescriptionCode
primary_tagDescriptionCode
source_tagDescriptionCode
has_tagDescriptionCode
add_tag_valueDescriptionCode
get_tag_valuesDescriptionCode
get_all_tagsDescriptionCode
remove_tagDescriptionCode
attach_seqDescriptionCode
seqDescriptionCode
entire_seqDescriptionCode
seq_idDescriptionCode
display_nameDescriptionCode
annotationDescriptionCode
get_SeqFeaturesDescriptionCode
add_SeqFeatureDescriptionCode
remove_SeqFeaturesDescriptionCode
gff_formatDescriptionCode
gff_stringDescriptionCode
slurp_gff_fileDescriptionCode
_from_gff_stringDescriptionCode
_expand_regionDescriptionCode
_parseDescriptionCode
_tag_valueDescriptionCode
seqname
No description
Code
display_id
No description
Code
all_tags
No description
Code
cleanup_generic
No description
Code
Methods description
set_attributescode    nextTop
 Title   : set_attributes
Usage :
Function: Sets a whole array of parameters at once.
Example :
Returns : none
Args : Named parameters, in the form as they would otherwise be passed
to new(). Currently recognized are:
-start start position -end end position -strand strand -phase the phase of the feature (0..2) -primary_tag primary tag -primary (synonym for -primary_tag) -source source tag -frame frame -score score value -tag a reference to a tag/value hash -gff_string GFF v.2 string to initialize from -gff1_string GFF v.1 string to initialize from -seq_id the display name of the sequence -annotation the AnnotationCollectionI object -location the LocationI object
direct_newcodeprevnextTop
 Title   : direct_new
Usage : my $feat = Bio::SeqFeature::Generic->direct_new;
Function: create a blessed hash - for performance improvement in
object creation
Returns : Bio::SeqFeature::Generic object
Args : none
locationcodeprevnextTop
 Title   : location
Usage : my $location = $feat->location();
Function: returns a location object suitable for identifying location
of feature on sequence or parent feature
Returns : Bio::LocationI object
Args : [optional] Bio::LocationI object to set the value to.
startcodeprevnextTop
 Title   : start
Usage : my $start = $feat->start;
$feat->start(20);
Function: Get/set on the start coordinate of the feature
Returns : integer
Args : none
endcodeprevnextTop
 Title   : end
Usage : my $end = $feat->end;
$feat->end($end);
Function: get/set on the end coordinate of the feature
Returns : integer
Args : none
lengthcodeprevnextTop
 Title   : length
Usage : my $len = $feat->length;
Function: Get the feature length computed as:
$feat->end - $feat->start + 1
Returns : integer
Args : none
strandcodeprevnextTop
 Title   : strand
Usage : my $strand = $feat->strand();
$feat->strand($strand);
Function: get/set on strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args : none
scorecodeprevnextTop
 Title   : score
Usage : my $score = $feat->score();
$feat->score($score);
Function: get/set on score information
Returns : float
Args : none if get, the new value if set
framecodeprevnextTop
 Title   : frame
Usage : my $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
primary_tagcodeprevnextTop
 Title   : primary_tag
Usage : my $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
source_tagcodeprevnextTop
 Title   : source_tag
Usage : my $tag = $feat->source_tag();
$feat->source_tag('genscan');
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : none
has_tagcodeprevnextTop
 Title   : has_tag
Usage : my $value = $feat->has_tag('some_tag');
Function: Tests wether a feature contaings a tag
Returns : TRUE if the SeqFeature has the tag,
and FALSE otherwise.
Args : The name of a tag
add_tag_valuecodeprevnextTop
 Title   : add_tag_value
Usage : $feat->add_tag_value('note',"this is a note");
Returns : TRUE on success
Args : tag (string) and one or more values (any scalar(s))
get_tag_valuescodeprevnextTop
 Title   : get_tag_values
Usage : my @values = $feat->get_tag_values('note');
Function: Returns a list of all the values stored
under a particular tag.
Returns : A list of scalars
Args : The name of the tag
get_all_tagscodeprevnextTop
 Title   : get_all_tags
Usage : my @tags = $feat->get_all_tags();
Function: Get a list of all the tags in a feature
Returns : An array of tag names
Args : none
# added a sort so that tags will be returned in a predictable order
# I still think we should be able to specify a sort function
# to the object at some point
# -js
remove_tagcodeprevnextTop
 Title   : remove_tag
Usage : $feat->remove_tag('some_tag');
Function: removes a tag from this feature
Returns : the array of values for this tag before removing it
Args : tag (string)
attach_seqcodeprevnextTop
 Title   : attach_seq
Usage : $feat->attach_seq($seq);
Function: Attaches a Bio::Seq object to this feature. This
Bio::Seq object is for the *entire* sequence: ie
from 1 to 10000
Example :
Returns : TRUE on success
Args : a Bio::PrimarySeqI compliant object
seqcodeprevnextTop
 Title   : seq
Usage : my $tseq = $feat->seq();
Function: returns the truncated sequence (if there) for this
Example :
Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence
bounded by start & end, or undef if there is no sequence attached
Args : none
entire_seqcodeprevnextTop
 Title   : entire_seq
Usage : my $whole_seq = $feat->entire_seq();
Function: gives the entire sequence that this seqfeature is attached to
Example :
Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
sequence attached
Args :
seq_idcodeprevnextTop
 Title   : seq_id
Usage : $feat->seq_id($newval)
Function: There are many cases when you make a feature that you
do know the sequence name, but do not know its actual
sequence. This is an attribute such that you can store
the ID (e.g., display_id) of the sequence.
This attribute should *not* be used in GFF dumping, as that should come from the collection in which the seq feature was found. Returns : value of seq_id Args : newvalue (optional)
display_namecodeprevnextTop
 Title   : display_name
Usage : my $featname = $feat->display_name;
Function: Implements the display_name() method, which is a human-readable
name for the feature.
Returns : value of display_name (a string)
Args : Optionally, on set the new value or undef
annotationcodeprevnextTop
 Title   : annotation
Usage : $feat->annotation($annot_obj);
Function: Get/set the annotation collection object for annotating this
feature.
Example : Returns : A Bio::AnnotationCollectionI object Args : newvalue (optional)
get_SeqFeaturescodeprevnextTop
 Title   : get_SeqFeatures
Usage : my @feats = $feat->get_SeqFeatures();
Function: Returns an array of sub Sequence Features
Returns : An array
Args : none
add_SeqFeaturecodeprevnextTop
 Title   : add_SeqFeature
Usage : $feat->add_SeqFeature($subfeat);
$feat->add_SeqFeature($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 parent's start/end/strand will be adjusted so that it grows to accommodate the new subFeature !IMPORTANT! The coordinates of the subfeature should not be relative to the parent feature it is attached to, but relative to the sequence the parent feature is located on. Returns : nothing Args : An object which has the SeqFeatureI interface
remove_SeqFeaturescodeprevnextTop
 Title   : remove_SeqFeatures
Usage : $feat->remove_SeqFeatures;
Function: Removes all SeqFeatures
If you want to remove only a subset of features then remove that subset from the returned array, and add back the rest. Example : Returns : The array of Bio::SeqFeatureI implementing features that was deleted. Args : none
gff_formatcodeprevnextTop
 Title   : gff_format
Usage : # get:
my $gffio = $feat->gff_format();
# set (change the default version of GFF2):
$feat->gff_format(Bio::Tools::GFF->new(-gff_version => 1));
Function: Get/set the GFF format interpreter. This object is supposed to
format and parse GFF. See Bio::Tools::GFF for the interface.
If this method is called as class method, the default for all newly created instances will be changed. Otherwise only this instance will be affected. Example : Returns : a Bio::Tools::GFF compliant object Args : On set, an instance of Bio::Tools::GFF or a derived object.
gff_stringcodeprevnextTop
 Title   : gff_string
Usage : my $str = $feat->gff_string;
my $str = $feat->gff_string($gff_formatter);
Function: Provides the feature information in GFF format.
We override this here from Bio::SeqFeatureI in order to use the formatter returned by gff_format(). Returns : A string Args : Optionally, an object implementing gff_string().
slurp_gff_filecodeprevnextTop
 Title   : slurp_file
Usage : my @features = Bio::SeqFeature::Generic::slurp_gff_file(\*FILE);
Function: Sneaky function to load an entire file as in memory objects.
Beware of big files.
This method is deprecated. Use Bio::Tools::GFF instead, which can also handle large files. Example : Returns : Args :
_from_gff_stringcodeprevnextTop
 Title   : _from_gff_string
Usage :
Function: Set feature properties from GFF string.
This method uses the object returned by gff_format() for the actual interpretation of the string. Set a different GFF format interpreter first if you need a specific version, like GFF1. (The default is GFF2.) Example : Returns : Args : a GFF-formatted string
_expand_regioncodeprevnextTop
 Title   : _expand_region
Usage : $feat->_expand_region($feature);
Function: Expand the total region covered by this feature to
accommodate for the given feature.
May be called whenever any kind of subfeature is added to this feature. add_SeqFeature() already does this. Returns : Args : A Bio::SeqFeatureI implementing object.
_parsecodeprevnextTop
 Title   : _parse
Usage :
Function: Parsing hints
Example :
Returns :
Args :
_tag_valuecodeprevnextTop
 Title   : _tag_value
Usage :
Function: For internal use only. Convenience method for those tags that
may only have a single value.
Returns : The first value under the given tag as a scalar (string)
Args : The tag as a string. Optionally, the value on set.
Methods code
newdescriptionprevnextTop
sub new {
    my ( $caller, @args) = @_;
    my ($self) = $caller->SUPER::new(@args);
    $self->_register_for_cleanup(\&cleanup_generic);
    $self->{'_parse_h'}       = {};
    $self->{'_gsf_tag_hash'}  = {};

    # bulk-set attributes
$self->set_attributes(@args); # done - we hope
return $self;
}
set_attributesdescriptionprevnextTop
sub set_attributes {
    my ($self,@args) = @_;
    my ($start, $end, $strand, $primary_tag, $source_tag, $primary, 
        $source, $frame, $score, $tag, $gff_string, $gff1_string,
        $seqname, $seqid, $annot, $location,$display_name, $pid,$phase) =
            $self->_rearrange([qw(START
                                  END
                                  STRAND
                                  PRIMARY_TAG
                                  SOURCE_TAG
                                  PRIMARY
                                  SOURCE
                                  FRAME
                                  SCORE
                                  TAG
                                  GFF_STRING
                                  GFF1_STRING
                                  SEQNAME
                                  SEQ_ID
                                  ANNOTATION
                                  LOCATION
                                  DISPLAY_NAME
                                  PRIMARY_ID
                                  PHASE
                                  )], @args);
    $location    && $self->location($location);
    $gff_string  && $self->_from_gff_string($gff_string);
    $gff1_string  && do {
        $self->gff_format(Bio::Tools::GFF->new('-gff_version' => 1));
        $self->_from_gff_stream($gff1_string);
    };
    
    $pid                    && $self->primary_id($pid);
    $primary_tag            && $self->primary_tag($primary_tag);
    $source_tag             && $self->source_tag($source_tag);
    $primary                && $self->primary_tag($primary);
    $source                 && $self->source_tag($source);
    defined $start          && $self->start($start);
    defined $end            && $self->end($end);
    defined $strand         && $self->strand($strand);
    defined $frame          && $self->frame($frame);
    defined $display_name   && $self->display_name($display_name);
    defined $score          && $self->score($score);
    $annot                  && $self->annotation($annot);
    if($seqname) {
        $self->warn("-seqname is deprecated. Please use -seq_id instead.");
        $seqid = $seqname unless $seqid;
    }
    $seqid          && $self->seq_id($seqid);
    $tag            && do {
        foreach my $t ( keys %$tag ) {
            $self->add_tag_value($t, UNIVERSAL::isa($tag->{$t}, "ARRAY") ? @{$tag->{$t}} : $tag->{$t});
        }
    };
    defined $phase          && $self->phase($phase);
}
direct_newdescriptionprevnextTop
sub direct_new {
    my ( $class) = @_;
    my ($self) = {};

    bless $self,$class;

    return $self;
}
locationdescriptionprevnextTop
sub location {
    my($self, $value ) = @_;  

    if (defined($value)) {
        unless (ref($value) and $value->isa('Bio::LocationI')) {
            $self->throw("object $value pretends to be a location but ".
                         "does not implement Bio::LocationI");
        }
        $self->{'_location'} = $value;
    }
    elsif (! $self->{'_location'}) {
        # guarantees a real location object is returned every time
$self->{'_location'} = Bio::Location::Simple->new(); } return $self->{'_location'};
}
startdescriptionprevnextTop
sub start {
    my ($self,$value) = @_;
    return $self->location->start($value);
}
enddescriptionprevnextTop
sub end {
    my ($self,$value) = @_;
    return $self->location->end($value);
}
lengthdescriptionprevnextTop
sub length {
    my $self = shift;
    return $self->end - $self->start() + 1;
}
stranddescriptionprevnextTop
sub strand {
    my $self = shift;
    return $self->location->strand(@_);
}
scoredescriptionprevnextTop
sub score {
    my $self = shift;

    if (@_) {
        my $value = shift;

        if ( defined $value && $value && $value !~ /^[A-Za-z]+$/ &&
            $value !~ /^[+-]?\d+\.?\d*(e-\d+)?/ and $value != 0) {
            $self->throw(-class=>'Bio::Root::BadParameter',
                         -text=>"'$value' is not a valid score",
                         -value=>$value);
        }
        if ($self->has_tag('score')) {
            $self->warn("Removing score value(s)");
            $self->remove_tag('score');
        }
        $self->add_tag_value('score',$value);
    }
    my ($score) = $self->has_tag('score') ? $self->get_tag_values('score') : undef;
    return $score;
}
framedescriptionprevnextTop
sub frame {
    my $self = shift;

    if ( @_ ) {
        my $value = shift;
        if ( defined $value && 
            $value !~ /^[0-2.]$/ ) {
            $self->throw("'$value' is not a valid frame");
        }
        if( defined $value && $value eq '.' ) { $value = '.' } 
        return $self->{'_gsf_frame'} = $value;
    }
    return $self->{'_gsf_frame'};
}
primary_tagdescriptionprevnextTop
sub primary_tag {
    my $self = shift;
    return $self->{'_primary_tag'} = shift if @_;
    return $self->{'_primary_tag'} || '';
}
source_tagdescriptionprevnextTop
sub source_tag {
    my $self = shift;
    return $self->{'_source_tag'} = shift if @_;
    return $self->{'_source_tag'} || '';
}
has_tagdescriptionprevnextTop
sub has_tag {
    my ($self, $tag) = @_;
    return exists $_[0]->{'_gsf_tag_hash'}->{$tag};
}
add_tag_valuedescriptionprevnextTop
sub add_tag_value {
    my $self = shift;
    my $tag = shift;
    $self->{'_gsf_tag_hash'}->{$tag} ||= [];
    push(@{$self->{'_gsf_tag_hash'}->{$tag}},@_);
}
get_tag_valuesdescriptionprevnextTop
sub get_tag_values {
    my ($self, $tag) = @_;

    if( ! defined $tag ) { return (); }
    if ( ! exists $self->{'_gsf_tag_hash'}->{$tag} ) {
        $self->throw("asking for tag value that does not exist $tag");
    }
    return @{$self->{'_gsf_tag_hash'}->{$tag}};
}
get_all_tagsdescriptionprevnextTop
sub get_all_tags {
    my ($self, @args) = @_;   
    return sort keys %{ $self->{'_gsf_tag_hash'}};
}
remove_tagdescriptionprevnextTop
sub remove_tag {
    my ($self, $tag) = @_;

    if ( ! exists $self->{'_gsf_tag_hash'}->{$tag} ) {
        $self->throw("trying to remove a tag that does not exist: $tag");
    }
    my @vals = @{$self->{'_gsf_tag_hash'}->{$tag}};
    delete $self->{'_gsf_tag_hash'}->{$tag};
    return @vals;
}
attach_seqdescriptionprevnextTop
sub attach_seq {
    my ($self, $seq) = @_;

    if ( ! ($seq && ref($seq) && $seq->isa("Bio::PrimarySeqI")) ) {
        $self->throw("Must attach Bio::PrimarySeqI objects to SeqFeatures but got '".ref($seq)."'");
    }

    $self->{'_gsf_seq'} = $seq;

    # attach to sub features if they want it
foreach ( $self->sub_SeqFeature() ) { $_->attach_seq($seq); } return 1;
}
seqdescriptionprevnextTop
sub seq {
    my ($self, $arg) = @_;

    if ( defined $arg ) {
        $self->throw("Calling SeqFeature::Generic->seq with an argument. You probably want attach_seq");
    }

    if ( ! exists $self->{'_gsf_seq'} ) {
        return;
    }

    # assumming our seq object is sensible, it should not have to yank
# the entire sequence out here.
my $seq = $self->{'_gsf_seq'}->trunc($self->start(), $self->end()); if ( defined $self->strand && $self->strand == -1 ) { # ok. this does not work well (?)
#print STDERR "Before revcom", $seq->str, "\n";
$seq = $seq->revcom; #print STDERR "After revcom", $seq->str, "\n";
} return $seq;
}
entire_seqdescriptionprevnextTop
sub entire_seq {
    return shift->{'_gsf_seq'};
}
seq_iddescriptionprevnextTop
sub seq_id {
    my $obj = shift;
    return $obj->{'_gsf_seq_id'} = shift if @_;
    return $obj->{'_gsf_seq_id'};
}
display_namedescriptionprevnextTop
sub display_name {
    my $self = shift;
    return $self->{'display_name'} = shift if @_;
    return $self->{'display_name'} || '';
}
annotationdescriptionprevnextTop
sub annotation {
    my ($obj,$value) = @_;

    # we are smart if someone references the object and there hasn't been
# one set yet
if(defined $value || ! defined $obj->{'annotation'} ) { $value = Bio::Annotation::Collection->new() unless ( defined $value ); $obj->{'annotation'} = $value; } return $obj->{'annotation'};
}
get_SeqFeaturesdescriptionprevnextTop
sub get_SeqFeatures {
    return @{ shift->{'_gsf_sub_array'} || []};
}
add_SeqFeaturedescriptionprevnextTop
sub add_SeqFeature {
    my ($self,$feat,$expand) = @_;
    unless( defined $feat ) {
        $self->warn("Called add_SeqFeature with no feature, ignoring");
        return;
    }
    if ( !$feat->isa('Bio::SeqFeatureI') ) {
        $self->warn("$feat does not implement Bio::SeqFeatureI. Will add it anyway, but beware...");
    }

    if($expand && ($expand eq 'EXPAND')) {
        $self->_expand_region($feat);
    } else {
        if ( !$self->contains($feat) ) {
            $self->throw("$feat is not contained within parent feature, and expansion is not valid");
        }
    }

    $self->{'_gsf_sub_array'} = [] unless exists($self->{'_gsf_sub_array'});
    push(@{$self->{'_gsf_sub_array'}},$feat);
}
remove_SeqFeaturesdescriptionprevnextTop
sub remove_SeqFeatures {
    my ($self) = @_;
    my @subfeats = @{$self->{'_gsf_sub_array'} || []};
    $self->{'_gsf_sub_array'} = []; # zap the array implicitly.
return @subfeats;
}
gff_formatdescriptionprevnextTop
sub gff_format {
    my ($self, $gffio) = @_;
    if(defined($gffio)) {
        if(ref($self)) {
            $self->{'_gffio'} = $gffio;
        } else {
            $Bio::SeqFeatureI::static_gff_formatter = $gffio;
        }
    }
    return (ref($self) && exists($self->{'_gffio'}) ?
            $self->{'_gffio'} : $self->_static_gff_formatter);
}
gff_stringdescriptionprevnextTop
sub gff_string {
    my ($self,$formatter) = @_;
    $formatter = $self->gff_format() unless $formatter;
    return $formatter->gff_string($self);
}
slurp_gff_filedescriptionprevnextTop
sub slurp_gff_file {
    my ($f) = @_;
    my @out;
    if ( !defined $f ) {
        Bio::Root::Root->throw("Must have a filehandle");
    }

    Bio::Root::Root->deprecated( -message => "deprecated method slurp_gff_file() called in Bio::SeqFeature::Generic. Use Bio::Tools::GFF instead.",
                                 -warn_version  => '1.005',
                                 -throw_version => '1.007',
                               );

    while(<$f>) {
        my $sf = Bio::SeqFeature::Generic->new('-gff_string' => $_);
        push(@out, $sf);
    }

    return @out;
}
_from_gff_stringdescriptionprevnextTop
sub _from_gff_string {
    my ($self, $string) = @_;
    $self->gff_format()->from_gff_string($self, $string);
}
_expand_regiondescriptionprevnextTop
sub _expand_region {
    my ($self, $feat) = @_;
    if(! $feat->isa('Bio::SeqFeatureI')) {
        $self->warn("$feat does not implement Bio::SeqFeatureI");
    }
    # if this doesn't have start set - forget it!
# changed to reflect sanity checks for LocationI
if(!$self->location->valid_Location) { $self->start($feat->start); $self->end($feat->end); $self->strand($feat->strand) unless $self->strand; } else { my ($start,$end,$strand) = $self->union($feat); $self->start($start); $self->end($end); $self->strand($strand); }
}
_parsedescriptionprevnextTop
sub _parse {
    my ($self) = @_;
    return $self->{'_parse_h'};
}
_tag_valuedescriptionprevnextTop
sub _tag_value {
    my $self = shift;
    my $tag = shift;

    if(@_ || (! $self->has_tag($tag))) {
        $self->remove_tag($tag) if($self->has_tag($tag));
        $self->add_tag_value($tag, @_);
    }
    return ($self->get_tag_values($tag))[0];
}


#######################################################################
# aliases for methods that changed their names in an attempt to make #
# bioperl names more consistent #
#######################################################################
}
seqnamedescriptionprevnextTop
sub seqname {
    my $self = shift;
    $self->warn("SeqFeatureI::seqname() is deprecated. Please use seq_id() instead.");
    return $self->seq_id(@_);
}
display_iddescriptionprevnextTop
sub display_id {
    my $self = shift;
    $self->warn("SeqFeatureI::display_id() is deprecated. Please use display_name() instead.");
    return $self->display_name(@_);
}

# this is towards consistent naming
}
all_tagsdescriptionprevnextTop
sub all_tags {
 return shift->get_all_tags(@_);
}
cleanup_genericdescriptionprevnextTop
sub cleanup_generic {
    my $self = shift;
    foreach my $f ( @{$self->{'_gsf_sub_array'} || []} ) {
        $f = undef;
    }
    $self->{'_gsf_seq'} = undef;
    foreach my $t ( keys %{$self->{'_gsf_tag_hash'} } ) {
        $self->{'_gsf_tag_hash'}->{$t} = undef;
        delete($self->{'_gsf_tag_hash'}->{$t}); # bug 1720 fix
} } 1;
}
General documentation
Implemented InterfacesTop
This class implements the following interfaces.
    Bio::SeqFeatureI
    Note that this includes implementing Bio::RangeI.
    Bio::AnnotatableI
    Bio::FeatureHolderI
    Features held by a feature are essentially sub-features.
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Ewan Birney <birney@sanger.ac.uk>
DEVELOPERSTop
This class has been written with an eye out for inheritance. The fields
the actual object hash are:
   _gsf_tag_hash  = reference to a hash for the tags
_gsf_sub_array = reference to an array for subfeatures
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Methods for implementing Bio::AnnotatableITop
Methods to implement Bio::FeatureHolderITop
This includes methods for retrieving, adding, and removing
features. Since this is already a feature, features held by this
feature holder are essentially sub-features.
GFF-related methodsTop