Bio::Cluster UniGene
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Summary
Bio::Cluster::UniGene - UniGene object
Package variables
Privates (from "my" definitions)
%species_map = ( 'Aga' => "Anopheles gambiae", 'Ame' => "Apis mellifera", 'At' => "Arabidopsis thaliana", 'Bmo' => "Bombyx mori", 'Bt' => "Bos taurus", 'Cel' => "Caenorhabditis elegans", 'Cfa' => "Canine familiaris", 'Cin' => "Ciona intestinalis", 'Cre' => "Chlamydomonas reinhardtii", 'Csa' => "Ciona savignyi", 'Csi' => "Citrus sinensis", 'Ddi' => "Dictyostelium discoideum", 'Dr' => "Danio rerio", 'Dm' => "Drosophila melanogaster", 'Gga' => "Gallus gallus", 'Gma' => "Glycine max", 'Han' => "Helianthus annus", 'Hs' => "Homo sapiens", 'Hma' => "Hydra magnipapillata", 'Hv' => "Hordeum vulgare", 'Lco' => "Lotus corniculatus", 'Les' => "Lycopersicon esculentum", 'Lsa' => "Lactuca sativa", 'Mdo' => "Malus x domestica", 'Mgr' => "Magnaporthe grisea", 'Mm' => "Mus musculus", 'Mtr' => "Medicago truncatula", 'Ncr' => "Neurospora crassa", 'Oar' => "Ovis aries", 'Omy' => "Oncorhynchus mykiss", 'Os' => "Oryza sativa", 'Ola' => "Oryzias latipes", 'Ppa' => "Physcomitrella patens", 'Pta' => "Pinus taeda", 'Ptp' => "Populus tremula x Populus tremuloides", 'Rn' => "Rattus norvegicus", 'Sbi' => "Sorghum bicolor", 'Sma' => "Schistosoma mansoni", 'Sof' => "Saccharum officinarum", 'Spu' => "Strongylocentrotus purpuratus", 'Ssa' => "Salmo salar", 'Ssc' => "Sus scrofa", 'Str' => "Xenopus tropicalis", 'Stu' => "Solanum tuberosum", 'Ta' => "Triticum aestivum", 'Tgo' => "Toxoplasma gondii", 'Tru' => "Takifugu rubripes", 'Vvi' => "Vitis vinifera", 'Xl' => "Xenopus laevis", 'Zm' => "Zea mays", )
Included modules
Bio::Annotation::Collection
Bio::Annotation::DBLink
Bio::Annotation::SimpleValue
Bio::Seq::SeqFactory
Bio::Species
Inherit
Bio::AnnotatableI Bio::Cluster::UniGeneI Bio::DescribableI Bio::Factory::SequenceStreamI Bio::IdentifiableI Bio::Root::Root
Synopsis
	use Bio::Cluster::UniGene;
use Bio::ClusterIO;
$stream = Bio::ClusterIO->new('-file' => "Hs.data", '-format' => "unigene"); # note: we quote -format to keep older perl's from complaining. while ( my $in = $stream->next_cluster() ) { print $in->unigene_id() . "\n"; while ( my $sequence = $in->next_seq() ) { print $sequence->accession_number() . "\n"; } }
Description
This UniGene object implements the Bio::Cluster::UniGeneI interface
for the representation if UniGene clusters in Bioperl. It is returned
by the Bio::ClusterIO parser for unigene format and contains all
the data associated with one UniGene record.
This class implements several interfaces and hence can be used
wherever instances of such interfaces are expected. In particular, the
interfaces are Bio::ClusterI as the base interface for all cluster
representations, and in addition Bio::IdentifiableI and
Bio::DescribableI.
The following lists the UniGene specific methods that are available
(see below for details). Be aware next_XXX iterators take a snapshot
of the array property when they are first called, and this snapshot is
not reset until the iterator is exhausted. Hence, once called you need
to exhaust the iterator to see any changes that have been made to the
property in the meantime. You will usually want to use the
non-iterator equivalents and loop over the elements yourself.
new() - standard new call
unigene_id() - set/get unigene_id
title() - set/get title (description)
gene() - set/get gene
cytoband() - set/get cytoband
mgi() - set/get mgi
locuslink() - set/get locuslink
homol() - set/get homologene
gnm_terminus() - set/get gnm_terminus
scount() - set/get scount
express() - set/get express, currently takes/returns a reference to an
array of expressed tissues
next_express() - returns the next tissue expression from the expressed
tissue array
chromosome() - set/get chromosome, currently takes/returns a reference
to an array of chromosome lines
next_chromosome() - returns the next chromosome line from the array of
chromosome lines
sts() - set/get sts, currently takes/returns a reference to an array
of sts lines
next_sts() - returns the next sts line from the array of sts lines
txmap() - set/get txmap, currently takes/returns a reference to an
array of txmap lines
next_txmap() - returns the next txmap line from the array of txmap
lines
protsim() - set/get protsim, currently takes/returns a reference to an
array of protsim lines
next_protsim() - returns the next protsim line from the array of
protsim lines
sequences() - set/get sequence, currently takes/returns a reference to
an array of references to seq info
next_seq() - returns a Seq object that currently only contains an
accession number
Methods
newDescriptionCode
unigene_idDescriptionCode
titleDescriptionCode
geneDescriptionCode
cytobandDescriptionCode
mgiDescriptionCode
locuslinkDescriptionCode
homolDescriptionCode
restr_exprDescriptionCode
gnm_terminusDescriptionCode
scountDescriptionCode
expressDescriptionCode
chromosomeDescriptionCode
stsDescriptionCode
txmapDescriptionCode
protsimDescriptionCode
sequencesDescriptionCode
speciesDescriptionCode
display_idDescriptionCode
descriptionDescriptionCode
sizeDescriptionCode
cluster_scoreDescriptionCode
get_membersDescriptionCode
annotationDescriptionCode
add_memberDescriptionCode
remove_membersDescriptionCode
next_locuslinkDescriptionCode
next_expressDescriptionCode
next_chromosomeDescriptionCode
next_protsimDescriptionCode
next_stsDescriptionCode
next_txmapDescriptionCode
_next_element
No description
Code
object_idDescriptionCode
versionDescriptionCode
authorityDescriptionCode
namespaceDescriptionCode
display_nameDescriptionCode
next_seqDescriptionCode
sequence_factoryDescriptionCode
_annotation_valueDescriptionCode
_annotation_value_aryDescriptionCode
_annotation_dblinkDescriptionCode
_remove_dblinkDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : used by ClusterIO
Returns : a new Bio::Cluster::Unigene object
unigene_idcodeprevnextTop
 Title   : unigene_id
Usage : unigene_id();
Function: Returns the unigene_id associated with the object.
Example : $id = $unigene->unigene_id or $unigene->unigene_id($id)
Returns : A string
Args : None or an id
titlecodeprevnextTop
 Title   : title
Usage : title();
Function: Returns the title associated with the object.
Example : $title = $unigene->title or $unigene->title($title)
Returns : A string
Args : None or a title
genecodeprevnextTop
 Title   : gene
Usage : gene();
Function: Returns the gene associated with the object.
Example : $gene = $unigene->gene or $unigene->gene($gene)
Returns : A string
Args : None or a gene
cytobandcodeprevnextTop
 Title   : cytoband
Usage : cytoband();
Function: Returns the cytoband associated with the object.
Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband)
Returns : A string
Args : None or a cytoband
mgicodeprevnextTop
 Title   : mgi
Usage : mgi();
Function: Returns the mgi associated with the object.
Example : $mgi = $unigene->mgi or $unigene->mgi($mgi)
Returns : A string
Args : None or a mgi
locuslinkcodeprevnextTop
 Title   : locuslink
Usage : locuslink();
Function: Returns or stores a reference to an array containing locuslink data.
Returns : An array reference
Args : None or an array reference
homolcodeprevnextTop
 Title   : homol
Usage : homol();
Function: Returns the homol entry associated with the object.
Example : $homol = $unigene->homol or $unigene->homol($homol)
Returns : A string
Args : None or a homol entry
restr_exprcodeprevnextTop
 Title   : restr_expr
Usage : restr_expr();
Function: Returns the restr_expr entry associated with the object.
Example : $restr_expr = $unigene->restr_expr or $unigene->restr_expr($restr_expr)
Returns : A string
Args : None or a restr_expr entry
gnm_terminuscodeprevnextTop
 Title   : gnm_terminus
Usage : gnm_terminus();
Function: Returns the gnm_terminus associated with the object.
Example : $gnm_terminus = $unigene->gnm_terminus or
$unigene->gnm_terminus($gnm_terminus)
Returns : A string
Args : None or a gnm_terminus
scountcodeprevnextTop
 Title   : scount
Usage : scount();
Function: Returns the scount associated with the object.
Example : $scount = $unigene->scount or $unigene->scount($scount)
Returns : A string
Args : None or a scount
expresscodeprevnextTop
 Title   : express
Usage : express();
Function: Returns or stores a reference to an array containing
tissue expression data
Returns : An array reference
Args : None or an array reference
chromosomecodeprevnextTop
 Title   : chromosome
Usage : chromosome();
Function: Returns or stores a reference to an array containing
chromosome lines
Returns : An array reference
Args : None or an array reference
stscodeprevnextTop
 Title   : sts
Usage : sts();
Function: Returns or stores a reference to an array containing sts lines
Returns : An array reference Args : None or an array reference
txmapcodeprevnextTop
 Title   : txmap
Usage : txmap();
Function: Returns or stores a reference to an array containing txmap lines
Returns : An array reference Args : None or an array reference
protsimcodeprevnextTop
 Title   : protsim
Usage : protsim();
Function: Returns or stores a reference to an array containing protsim lines
This should really only be used by ClusterIO, not directly
Returns : An array reference
Args : None or an array reference
sequencescodeprevnextTop
 Title   : sequences
Usage : sequences();
Function: Returns or stores a reference to an array containing
sequence data.
This is mostly reserved for ClusterIO parsers. You should use get_members() for get and add_member()/remove_members() for set. Returns : An array reference, or undef Args : None or an array reference or undef
speciescodeprevnextTop
 Title   : species
Usage : $obj->species($newval)
Function: Get/set the species object for this Unigene cluster.
Example :
Returns : value of species (a Bio::Species object)
Args : on set, new value (a Bio::Species object or
the binomial name, or undef, optional)
display_idcodeprevnextTop
 Title   : display_id
Usage :
Function: Get/set the display name or identifier for the cluster
This is aliased to unigene_id(). Returns : a string Args : optional, on set the display ID ( a string)
description()codeprevnextTop
 Title   : description
Usage : $string = $obj->description()
Function: A text string suitable for displaying to the user a
description. This string is likely to have spaces, but
should not have any newlines or formatting - just plain
text. The string should not be greater than 255 characters
and clients can feel justified at truncating strings at 255
characters for the purposes of display
This is already demanded by Bio::ClusterI and hence is present anyway. Returns : A scalar
sizecodeprevnextTop
 Title   : size
Usage : Bio::ClusterI->size();
Function: get for the size of the family,
calculated from the number of members
This is aliased to scount(). Returns : the size of the cluster Args :
cluster_scorecodeprevnextTop
 Title   : cluster_score
Usage : $cluster ->cluster_score(100);
Function: get/set for cluster_score which
represent the score in which the clustering
algorithm assigns to this cluster.
For UniGene clusters, there really is no cluster score that would come with the data. However, we provide an implementation here so that you can score UniGene clusters if you want to. Returns : a number Args : optionally, on set a number
get_memberscodeprevnextTop
 Title   : get_members
Usage : Bio::ClusterI->get_members(($seq1, $seq2));
Function: retrieve the members of the family by some criteria
Will return all members if no criteria are provided. At this time this implementation does not support specifying criteria and will always return all members. Returns : the array of members Args :
annotationcodeprevnextTop
 Title   : annotation
Usage : $obj->annotation($newval)
Function: Get/set the Bio::AnnotationCollectionI object for
this UniGene cluster.
Many attributes of this class are actually stored within the annotation collection object as Bio::AnnotationI
compliant objects, so you can conveniently access them
through the same interface as you would e.g. access
Bio::SeqI annotation properties.
If you call this method in set mode and replace the annotation collection with another one you should know exactly what you are doing. Example : Returns : a Bio::AnnotationCollectionI compliant object
Args : on set, new value (a Bio::AnnotationCollectionI
compliant object or undef, optional)
add_membercodeprevnextTop
 Title   : add_member
Usage :
Function: Adds a member object to the list of members.
Example :
Returns : TRUE if the new member was successfuly added, and FALSE
otherwise.
Args : The member to add.
remove_memberscodeprevnextTop
 Title   : remove_members
Usage :
Function: Remove the list of members for this cluster such that the
member list is undefined afterwards (as opposed to zero members).
Example :
Returns : the previous list of members
Args : none
next_locuslinkcodeprevnextTop
 Title   : next_locuslink
Usage : next_locuslink();
Function: Returns the next locuslink from an array referred
to using $obj->{'locuslink'}
If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $locuslink = $in->next_locuslink() ) { print "$locuslink\n"; } Returns : String Args : None
next_expresscodeprevnextTop
 Title   : next_express
Usage : next_express();
Function: Returns the next tissue from an array referred
to using $obj->{'express'}
If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $express = $in->next_express() ) { print "$express\n"; } Returns : String Args : None
next_chromosomecodeprevnextTop
 Title   : next_chromosome
Usage : next_chromosome();
Function: Returns the next chromosome line from an array referred
to using $obj->{'chromosome'}
If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $chromosome = $in->next_chromosome() ) { print "$chromosome\n"; } Returns : String Args : None
next_protsimcodeprevnextTop
 Title   : next_protsim
Usage : next_protsim();
Function: Returns the next protsim line from an array referred
to using $obj->{'protsim'}
If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $protsim = $in->next_protsim() ) { print "$protsim\n"; } Returns : String Args : None
next_stscodeprevnextTop
 Title   : next_sts
Usage : next_sts();
Function: Returns the next sts line from an array referred
to using $obj->{'sts'}
If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $sts = $in->next_sts() ) { print "$sts\n"; } Returns : String Args : None
next_txmapcodeprevnextTop
 Title   : next_txmap
Usage : next_txmap();
Function: Returns the next txmap line from an array
referred to using $obj->{'txmap'}
If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $tsmap = $in->next_txmap() ) { print "$txmap\n"; } Returns : String Args : None
object_idcodeprevnextTop
 Title   : object_id
Usage : $string = $obj->object_id()
Function: a string which represents the stable primary identifier
in this namespace of this object. For DNA sequences this
is its accession_number, similarly for protein sequences
This is aliased to unigene_id(). Returns : A scalar
versioncodeprevnextTop
 Title   : version
Usage : $version = $obj->version()
Function: a number which differentiates between versions of
the same object. Higher numbers are considered to be
later and more relevant, but a single object described
the same identifier should represent the same concept
Unigene clusters usually won't have a version, so this will be mostly undefined. Returns : A number Args : on set, new value (a scalar or undef, optional)
authoritycodeprevnextTop
 Title   : authority
Usage : $authority = $obj->authority()
Function: a string which represents the organisation which
granted the namespace, written as the DNS name for
organisation (eg, wormbase.org)
Returns : A scalar Args : on set, new value (a scalar or undef, optional)
namespacecodeprevnextTop
 Title   : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection
Returns : A scalar Args : on set, new value (a scalar or undef, optional)
display_namecodeprevnextTop
 Title   : display_name
Usage : $string = $obj->display_name()
Function: A string which is what should be displayed to the user
the string should have no spaces (ideally, though a cautious
user of this interface would not assumme this) and should be
less than thirty characters (though again, double checking
this is a good idea)
This is aliased to unigene_id(). Returns : A scalar Status : Virtual
next_seqcodeprevnextTop
 Title   : next_seq
Usage : next_seq();
Function: Returns the next seq as a Seq object as defined by
$seq->sequence_factory(),
at present an empty Bio::Seq::RichSeq object with
just the accession_number() and pid() set
This iterator will not exhaust the array of member sequences. If you call next_seq() again after it returned undef, it will re-cycle through the list of member sequences. Example : while ( my $sequence = $in->next_seq() ) { print $sequence->accession_number() . "\n"; } Returns : Bio::PrimarySeqI object Args : None
sequence_factorycodeprevnextTop
 Title   : sequence_factory
Usage : $seqio->sequence_factory($seqfactory)
Function: Get/Set the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args : [optional] Bio::Factory::SequenceFactoryI
_annotation_valuecodeprevnextTop
 Title   : _annotation_value
Usage :
Function: Private method.
Example :
Returns : the value (a string)
Args : annotation key (a string)
on set, annotation value (a string)
_annotation_value_arycodeprevnextTop
 Title   : _annotation_value_ary
Usage :
Function: Private method.
Example :
Returns : reference to the array of values
Args : annotation key (a string)
on set, reference to an array holding the values
_annotation_dblinkcodeprevnextTop
 Title   : _annotation_dblink
Usage :
Function: Private method.
Example :
Returns : array of accessions for the given database (namespace)
Args : annotation key (a string)
dbname (a string) (optional on get, mandatory on set)
on set, accession or ID (a string), and version
_remove_dblinkcodeprevnextTop
 Title   : _remove_dblink
Usage :
Function: Private method.
Example :
Returns : array of accessions for the given database (namespace)
Args : annotation key (a string)
dbname (a string) (optional)
Methods code
newdescriptionprevnextTop
sub new {
    # standard new call..
my($caller,@args) = @_; my $self = $caller->SUPER::new(@args); my ($ugid,$desc,$mems,$size,$species,$dispid,$id,$ns,$auth,$v,$seqfact) = $self->_rearrange([qw(UNIGENE_ID DESCRIPTION MEMBERS SIZE SPECIES DISPLAY_ID OBJECT_ID NAMESPACE AUTHORITY VERSION SEQFACTORY )], @args); $self->{'_alphabet'} = 'dna'; $self->unigene_id($ugid) if $ugid; $self->description($desc) if $desc; $self->sequences($mems) if $mems; $self->size($size) if defined($size); $self->display_id($dispid) if $dispid; # overwrites ugid
$self->object_id($id) if $id; # overwrites dispid
$self->namespace($ns || 'UniGene'); $self->authority($auth || 'NCBI'); $self->version($v) if defined($v); if( ! defined $seqfact ) { $seqfact = Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq'); } $self->sequence_factory($seqfact); if( (! $species) && (defined $self->unigene_id() && $self->unigene_id() =~ /^([A-Za-z]+)\.[0-9]/)) { # try set a default one depending on the ID
$species = $species_map{$1}; } $self->species($species); return $self;
}
unigene_iddescriptionprevnextTop
sub unigene_id {
	my ($obj,$value) = @_;
	if( defined $value) {
		$obj->{'unigene_id'} = $value;
	}
	return $obj->{'unigene_id'};
}
titledescriptionprevnextTop
sub title {
	my ($obj,$value) = @_;
	if( defined $value) {
		$obj->{'title'} = $value;
	}
	return $obj->{'title'};
}
genedescriptionprevnextTop
sub gene {
    my $self = shift;
    return $self->_annotation_value('gene_name', @_);
}
cytobanddescriptionprevnextTop
sub cytoband {
    my $self = shift;
    return $self->_annotation_value('cyto_band', @_);
}
mgidescriptionprevnextTop
sub mgi {
    my $self = shift;
    my $acc;

    if(@_) {
	# purge first
$self->_remove_dblink('dblink','MGI'); # then add if a valid value is present
if($acc = shift) { $self->_annotation_dblink('dblink','MGI',$acc); } } else { ($acc) = $self->_annotation_dblink('dblink','MGI'); } return $acc;
}
locuslinkdescriptionprevnextTop
sub locuslink {
    my ($self,$ll) = @_;
    
    if($ll) {
	# purge first
$self->_remove_dblink('dblink','LocusLink'); # then add as many accessions as are present
foreach my $acc (@$ll) { $self->_annotation_dblink('dblink','LocusLink',$acc); } } else { my @accs = $self->_annotation_dblink('dblink','LocusLink'); $ll = [@accs]; } return $ll;
}
homoldescriptionprevnextTop
sub homol {
    my $self = shift;
    return $self->_annotation_value('homol', @_);
}
restr_exprdescriptionprevnextTop
sub restr_expr {
    my $self = shift;
    return $self->_annotation_value('restr_expr', @_);
}
gnm_terminusdescriptionprevnextTop
sub gnm_terminus {
    my $self = shift;
    return $self->_annotation_value('gnm_terminus', @_);
}
scountdescriptionprevnextTop
sub scount {
	my ($obj,$value) = @_;
	if( defined $value) {
	    $obj->{'scount'} = $value;
	} elsif((! defined($obj->{'scount'})) && defined($obj->sequences())) {
	    $obj->{'scount'} = $obj->size();
	}
	return $obj->{'scount'};
}
expressdescriptionprevnextTop
sub express {
    my $self = shift;

    return $self->_annotation_value_ary('expressed',@_);
}
chromosomedescriptionprevnextTop
sub chromosome {
    my $self = shift;

    return $self->_annotation_value_ary('chromosome',@_);
}
stsdescriptionprevnextTop
sub sts {
    my $self = shift;

    return $self->_annotation_value_ary('sts',@_);
}
txmapdescriptionprevnextTop
sub txmap {
    my $self = shift;

    return $self->_annotation_value_ary('txmap',@_);
}
protsimdescriptionprevnextTop
sub protsim {
    my $self = shift;

    return $self->_annotation_value_ary('protsim',@_);
}
sequencesdescriptionprevnextTop
sub sequences {
    my $self = shift;

    return $self->{'members'} = shift if @_;
    return $self->{'members'};
}
speciesdescriptionprevnextTop
sub species {
    my $self = shift;

    if(@_) {
	my $species = shift;
	if($species && (! ref($species))) {
	    my @class = reverse(split(' ',$species));
	    $species = Bio::Species->new(-classification =>\@ class);
	}
	return $self->{'species'} = $species;
    }
    return $self->{'species'};
}
display_iddescriptionprevnextTop
sub display_id {
    return shift->unigene_id(@_);
}
descriptiondescriptionprevnextTop
sub description {
    return shift->title(@_);
}
sizedescriptionprevnextTop
sub size {
    my $self = shift;

    # hard-wiring the size is allowed if there are no sequences
return $self->scount(@_) unless defined($self->sequences()); # but we can't change the number of members through this method
my $n = scalar(@{$self->sequences()}); if(@_ && ($n != $_[0])) { $self->throw("Cannot change cluster size using size() from $n to ". $_[0]); } return $n;
}
cluster_scoredescriptionprevnextTop
sub cluster_score {
    my $self = shift;

    return $self->{'cluster_score'} = shift if @_;
    return $self->{'cluster_score'};
}
get_membersdescriptionprevnextTop
sub get_members {
    my $self = shift;

    my $mems = $self->sequences() || [];
    # already objects?
if(@$mems && (ref($mems->[0]) eq "HASH")) { # nope, we need to build the object list from scratch
my @memlist = (); while(my $seq = $self->next_seq()) { push(@memlist, $seq); } # we cache this array of objects as the new member list
$mems =\@ memlist; $self->sequences($mems); } # done
return @$mems;
}
annotationdescriptionprevnextTop
sub annotation {
    my $self = shift;

    if(@_) {
	return $self->{'annotation'} = shift;
    } elsif(! exists($self->{'annotation'})) {
	$self->{'annotation'} = Bio::Annotation::Collection->new();
    }
    return $self->{'annotation'};
}
add_memberdescriptionprevnextTop
sub add_member {
    my ($self,@mems) = @_;

    my $memlist = $self->{'members'} || [];
    # this is an object interface; is the member list already objects?
if(@$memlist && (ref($memlist->[0]) eq "HASH")) { # nope, convert to objects
$memlist = [$self->get_members()]; } # add new member(s)
push(@$memlist, @mems); # store if we created this array ref ourselves
$self->sequences($memlist); # done
return 1;
}
remove_membersdescriptionprevnextTop
sub remove_members {
    my $self = shift;

    my @mems = $self->get_members();
    $self->sequences(undef);
    return @mems;
}
next_locuslinkdescriptionprevnextTop
sub next_locuslink {
    my ($obj) = @_;

    return $obj->_next_element("ll","locuslink");
}
next_expressdescriptionprevnextTop
sub next_express {
    my ($obj) = @_;

    return $obj->_next_element("express","express");
}
next_chromosomedescriptionprevnextTop
sub next_chromosome {
    my ($obj) = @_;

    return $obj->_next_element("chr","chromosome");
}
next_protsimdescriptionprevnextTop
sub next_protsim {
    my ($obj) = @_;

    return $obj->_next_element("protsim","protsim");
}
next_stsdescriptionprevnextTop
sub next_sts {
    my ($obj) = @_;

    return $obj->_next_element("sts","sts");
}
next_txmapdescriptionprevnextTop
sub next_txmap {
    my ($obj) = @_;

    return $obj->_next_element("txmap","txmap");
}

###############################
# private method
#
# args: prefix name for the queue
# name of the method from which to re-fill
# returns: the next element from that queue, or undef if the queue is empty
###############################
}
_next_elementdescriptionprevnextTop
sub _next_element {
    my ($self,$queuename,$meth) = @_;

    $queuename = "_".$queuename."_queue";
    if(! exists($self->{$queuename})) {
	# re-initialize from array of sequence data
$self->{$queuename} = [@{$self->$meth() }]; } my $queue = $self->{$queuename}; # is queue exhausted (equivalent to end of stream)?
if(! @$queue) { # yes, remove queue and signal to the caller
delete $self->{$queuename}; return; } return shift(@$queue);
}
object_iddescriptionprevnextTop
sub object_id {
    return shift->unigene_id(@_);
}
versiondescriptionprevnextTop
sub version {
    my $self = shift;

    return $self->{'version'} = shift if @_;
    return $self->{'version'};
}
authoritydescriptionprevnextTop
sub authority {
    my $self = shift;

    return $self->{'authority'} = shift if @_;
    return $self->{'authority'};
}
namespacedescriptionprevnextTop
sub namespace {
    my $self = shift;

    return $self->{'namespace'} = shift if @_;
    return $self->{'namespace'};
}
display_namedescriptionprevnextTop
sub display_name {
    return shift->unigene_id(@_);
}
next_seqdescriptionprevnextTop
sub next_seq {
    my ($obj) = @_;

    if(! exists($obj->{'_seq_queue'})) {
	# re-initialize from array of sequence data
$obj->{'_seq_queue'} = [@{$obj->sequences()}]; } my $queue = $obj->{'_seq_queue'}; # is queue exhausted (equivalent to end of stream)?
if(! @$queue) { # yes, remove queue and signal to the caller
delete $obj->{'_seq_queue'}; return; } # no, still data in the queue: get the next one from the queue
my $seq_h = shift(@$queue); # if this is not a simple hash ref, it's an object already, and we'll
# return just that
return $seq_h if(ref($seq_h) ne 'HASH'); # nope, we need to assemble this object from scratch
#
# assemble the annotation collection
my $ac = Bio::Annotation::Collection->new(); foreach my $k (keys %$seq_h) { next if $k =~ /acc|pid|nid|version/; my $ann = Bio::Annotation::SimpleValue->new(-tagname => $k, -value => $seq_h->{$k}); $ac->add_Annotation($ann); } # assemble the initialization parameters and create object
my $seqobj = $obj->sequence_factory->create( -accession_number => $seq_h->{acc}, -pid => $seq_h->{pid}, # why does NCBI prepend a 'g' to its own identifiers??
-primary_id => $seq_h->{nid} && $seq_h->{nid} =~ /^g\d+$/ ? substr($seq_h->{nid},1) : $seq_h->{nid}, -display_id => $seq_h->{acc}, -seq_version => $seq_h->{version}, -alphabet => $obj->{'_alphabet'}, -namespace => $seq_h->{acc} =~ /^NM_/ ? 'RefSeq' : 'GenBank', -authority => $obj->authority(), # default is NCBI
-species => $obj->species(), -annotation => $ac ); return $seqobj;
}
sequence_factorydescriptionprevnextTop
sub sequence_factory {
    my ($self,$obj) = @_;   
    if( defined $obj ) {
	if( ! ref($obj) || ! $obj->isa('Bio::Factory::SequenceFactoryI') ) {
	    $self->throw("Must provide a valid Bio::Factory::SequenceFactoryI object to ".ref($self)." sequence_factory()");
	}
	$self->{'_seqfactory'} = $obj;
    }
    $self->{'_seqfactory'};
}
_annotation_valuedescriptionprevnextTop
sub _annotation_value {
    my $self = shift;
    my $key = shift;

    my ($ann, $val);
    if(@_) {
	$val = shift;
	if(! defined($val)) {
	    ($ann) = $self->annotation->remove_Annotations($key);
	    return $ann ? $ann->value() : undef;
	}
    }
    ($ann) = $self->annotation->get_Annotations($key);
    if(defined $ann && (! $val)) {
	# get mode and exists
$val = $ann->value(); } elsif($val) { # set mode
if(!defined $ann) { $ann = Bio::Annotation::SimpleValue->new(-tagname => $key); $self->annotation->add_Annotation($ann); } $ann->value($val); } return $val;
}
_annotation_value_arydescriptionprevnextTop
sub _annotation_value_ary {
    my ($self,$key,$arr) = @_;

    my $ac = $self->annotation;
    if($arr) {
	# purge first
$ac->remove_Annotations($key); # then add as many values as are present
foreach my $val (@$arr) { my $ann = Bio::Annotation::SimpleValue->new(-value => $val, -tagname => $key ); $ac->add_Annotation($ann); } } else { my @vals = map { $_->value(); } $ac->get_Annotations($key); $arr = [@vals]; } return $arr;
}
_annotation_dblinkdescriptionprevnextTop
sub _annotation_dblink {
    my ($self,$key,$dbname,$acc,$version) = @_;

    if($acc) {
	# set mode -- this is adding here
my $ann = Bio::Annotation::DBLink->new(-tagname => $key, -primary_id => $acc, -database => $dbname, -version => $version); $self->annotation->add_Annotation($ann); return 1; } else { # get mode
my @anns = $self->annotation->get_Annotations($key); # filter out those that don't match the requested database
if($dbname) { @anns = grep { $_->database() eq $dbname; } @anns; } return map { $_->primary_id(); } @anns; }
}
_remove_dblinkdescriptionprevnextTop
sub _remove_dblink {
    my ($self,$key,$dbname) = @_;

    my $ac = $self->annotation();
    my @anns = ();
    if($dbname) {
	foreach my $ann ($ac->remove_Annotations($key)) {
	    if($ann->database() eq $dbname) {
		push(@anns, $ann);
	    } else {
		$ac->add_Annotation($ann);
	    }
	}
    } else {
	@anns = $ac->remove_Annotations($key);
    }
    return map { $_->primary_id(); } @anns;
}


#####################################################################
# aliases for naming consistency or other reasons #
#####################################################################
*sequence =\& sequences; 1;
}
General documentation
Implemented InterfacesTop
This class implementes the following interfaces.
    Bio::Cluster::UniGeneI
    This includes implementing Bio::ClusterI.
    Bio::IdentifiableI
    Bio::DescribableI
    Bio::AnnotatableI
    Bio::Factory::SequenceStreamI
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 - Andrew MacgregorTop
Email andrew at cbbc.murdoch.edu.au
CONTRIBUTORSTop
Hilmar Lapp, hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
Bio::Cluster::UniGeneI methodsTop
Bio::ClusterI methodsTop
Annotatable view at the object propertiesTop
Implementation specific methodsTop
 These are mostly for adding/removing to array properties, and for
methods with special functionality.
Bio::IdentifiableI methodsTop
Bio::DescribableI methodsTop
Bio::Factory::SequenceStreamI methodsTop
Private methodsTop