Raw content of Bio::EnsEMBL::MiscFeature
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::MiscFeature - A miscelaneous feature with arbitrary features and
associations.
=head1 SYNOPSIS
use Bio::EnsEMBL::MiscFeature;
use Bio::EnsEMBL::MiscSet;
use Bio::EnsEMBL::Attribute;
my $mfeat = Bio::EnsEMBL::MiscFeature->new(
-START => 1200,
-END => 100_000,
-STRAND => 1,
-SLICE => $slice
);
# Can add attributes to the misc feature and associate with various
# sets
my $clone_set = Bio::EnsEMBL::MiscSet->new(
-CODE => 'clone',
-NAME => '1MB clone set',
-DESCRIPTION => '1MB CloneSet'
);
my $tiling_path_set = Bio::EnsEMBL::MiscSet->new(
-CODE => 'tilingpath',
-NAME => 'tiling path set'
);
my $attrib1 = Bio::EnsEMBL::Attribute->new(
-VALUE => 'RLX12451',
-CODE => 'name',
-NAME => 'name'
);
my $attrib2 = Bio::EnsEMBL::Attribute->new(
-VALUE => '4',
-CODE => 'version',
-NAME => 'version'
);
my $attrib3 = Bio::EnsEMBL::Attribute->new(
-VALUE => 'AL42131.4',
-CODE => 'synonym',
-NAME => 'synonym'
);
# can associate a misc feature with any number of sets
$mfeat->add_MiscSet($clone_set);
$mfeat->add_MiscSet($tiling_path_set);
# can add arbitrary attributes to a misc feature
$mfeat->add_Attribute($attrib1);
$mfeat->add_Attribute($attrib2);
$mfeat->add_Attribute($attrib3);
my ($name_attrib) = @{ $mfeat->get_all_Attributes('name') };
my @all_attribs = @{ $mfeat->get_all_Attributes() };
my @all_sets = @{ $mfeat->get_all_MiscSets() };
my ($clone_set) = @{ $mfeat->get_all_CloneSets('clone') };
# Can do normal feature operations as well
$mfeat = $mfeat->transform('supercontig');
print $mfeat->slice->seq_region_name, ' ', $mfeat->start, '-',
$mfeat->end;
=head1 DESCRIPTION
MiscFeatures are extremely general features with a location, and an
arbitrary group of attributes. They are grouped with other features of
the same 'type' through the use of MiscSets (see Bio::EnsEMBL::MiscSet).
Attributes are attached in the fom of Bio::EnsEMBL::Attribute objects.
See Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor for ways to fetch or store
MiscFeatures.
=cut
package Bio::EnsEMBL::MiscFeature;
use strict;
use warnings;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Exception qw(throw);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Feature);
=head2 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::MiscFeature->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::MiscFeature
Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND ,-ADAPTOR arguments
Caller : general, subclass constructors
Status : Stable
=cut
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
$self->{'attributes'} = [];
return $self;
}
=head2 new_fast
Arg [...] : hashref to bless as new MiscFeature
Example : $miscfeature = Bio::EnsEMBL::MiscFeature->new_fast();
Description: Creates a new Miscfeature.
Returntype : Bio::EnsEMBL::MiscFeature
Exceptions : none
Caller : general
Status : Stable
=cut
sub new_fast {
my $class = shift;
my $hashref = shift;
$hashref->{'attributes'} ||= [];
return bless($hashref, $class);
}
=head2 add_Attribute
Arg [1] : Bio::EnsEMBL::Attribute $attribute
Example : $misc_feature->add_attribute($attribute);
Description: Adds an attribute to this misc. feature
Returntype : none
Exceptions : throw on wrong argument type
Caller : general
Status : Stable
=cut
sub add_Attribute {
my ($self, $attrib) = @_;
if( ! defined $attrib || ! $attrib->isa( "Bio::EnsEMBL::Attribute" )) {
throw( "You have to provide a Bio::EnsEMBL::Attribute, not a [$attrib]" );
}
$self->{'attributes'} ||= [];
push @{$self->{'attributes'}}, $attrib
}
=head2 add_MiscSet
Arg [1] : Bio::EnsEMBL::MiscSet $set
The set to add
Example : $misc_feature->add_MiscSet(Bio::EnsEMBL::MiscSet->new(...));
Description: Associates this MiscFeature with a given Set.
Returntype : none
Exceptions : throw if the set arg is not provided,
throw if the set to be added does not have a code
Caller : general
Status : Stable
=cut
sub add_MiscSet {
my $self = shift;
my $miscSet = shift;
if(!$miscSet || !ref($miscSet) || !$miscSet->isa('Bio::EnsEMBL::MiscSet')) {
throw('Set argument must be a Bio::EnsEMBL::MiscSet');
}
$self->{'miscSets'} ||= [];
push( @{$self->{'miscSets'}}, $miscSet );
}
=head2 get_all_MiscSets
Arg [1] : optional string $code
The code of the set to retrieve
Example : $set = $misc_feature->get_all_MiscSets($code);
Description: Retrieves a set that this feature is associated with via its
code. Can return empty lists. Usually returns about one elements lists.
Returntype : listref of Bio::EnsEMBL::MiscSet
Exceptions : throw if the code arg is not provided
Caller : general
Status : Stable
=cut
sub get_all_MiscSets {
my $self = shift;
my $code = shift;
$self->{'miscSets'} ||= [];
if( defined $code ) {
my @results = grep { uc($_->code())eq uc( $code ) } @{$self->{'miscSets'}};
return \@results;
} else {
return $self->{'miscSets'};
}
}
=head2 get_all_Attributes
Arg [1] : optional string $code
The code of the Attribute objects to retrieve
Example : @attributes = $misc_feature->get_all_Attributes('name');
Description: Retrieves a list of Attribute objects for given code or all
of the associated Attributes.
Returntype : listref of Bio::EnsEMBL::Attribute
Exceptions :
Caller : general
Status : Stable
=cut
sub get_all_Attributes {
my $self = shift;
my $code = shift;
my @results;
my $result;
if( defined $code ) {
@results = grep { uc( $_->code() ) eq uc( $code )} @{$self->{'attributes'}};
return \@results;
} else {
return $self->{'attributes'};
}
}
=head2 get_all_attribute_values
Arg [1] : string $code
The code of the Attribute object values to retrieve
Example : @attributes_vals = @{$misc_feature->get_all_attribute_values('name')};
Description: Retrieves a list of Attribute object values for given code or all
of the associated Attributes.
Returntype : listref of values
Exceptions :
Caller : general
Status : Stable
=cut
sub get_all_attribute_values {
my $self = shift;
my $code = shift;
my @results = map { uc( $_->code() ) eq uc( $code ) ? $_->value : () }
@{$self->{'attributes'}};
return \@results;
}
=head2 get_scalar_attribute
Arg [1] : string $code
The code of the Attribute object values to retrieve
Example : $vals = $misc_feature->get_scalar_attribute('name');
Description: Retrieves a value for given code or all
of the associated Attributes.
Returntype : scalar value
Exceptions :
Caller : general
Status : Stable
=cut
sub get_scalar_attribute {
my $self = shift;
my $code = shift;
my @results = grep { uc( $_->code() ) eq uc( $code )} @{$self->{'attributes'}};
return @results ? $results[0]->value() : '';
}
sub get_first_scalar_attribute {
my $self = shift;
foreach my $code ( @_ ) {
my @results = grep { uc( $_->code() ) eq uc( $code )} @{$self->{'attributes'}};
return $results[0]->value() if @results;
}
return '';
}
=head2 display_id
Arg [1] : none
Example : print $kb->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For misc_features this is the first
name or synonym attribute or '' if neither are defined.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub display_id {
my $self = shift;
my ($attrib) = @{$self->get_all_Attributes('name')};
($attrib) = @{$self->get_all_Attributes('synonym')} if(!$attrib);
if( defined $attrib ) {
return $attrib->value();
} else {
return '';
}
}
1;
]]>