Bio::Cluster
UniGene
Summary
Bio::Cluster::UniGene - UniGene object
Package variables
Privates (from "my" definitions)
%species_map = ( 'Aga' => "Anopheles gambiae", 'At' => "Arabidopsis thaliana", 'Bt' => "Bos taurus", 'Cel' => "Caenorhabditis elegans", 'Cin' => "Ciona intestinalis", 'Cre' => "Chlamydomonas reinhardtii", 'Ddi' => "Dictyostelium discoideum", 'Dr' => "Danio rerio", 'Dm' => "Drosophila melanogaster", 'Gga' => "Gallus gallus", 'Gma' => "Glycine max", 'Hs' => "Homo sapiens", 'Hv' => "Hordeum vulgare", 'Les' => "Lycopersicon esculentum", 'Mtr' => "Medicago truncatula", 'Mm' => "Mus musculus", 'Os' => "Oryza sativa", 'Ola' => "Oryzias latipes", 'Rn' => "Rattus norvegicus", 'Str' => "Silurana tropicalis", 'Sbi' => "Sorghum bicolor", 'Ssc' => "Sus scrofa", 'Ta' => "Triticum aestivum", 'Xl' => "Xenopus laevis", 'Zm' => "Zea mays", )
Included modules
Inherit
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
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
Methods description
Title : new
Usage : used by ClusterIO
Returns : a new Bio::Cluster::Unigene object |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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) |
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) |
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 |
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 : |
Title : cluster_score
Usage : $cluster ->cluster_score(100);
Function: get/set for cluster_score which
represent the score in which the clustering
algorithm assigns to this cluster.
For UniGene clusters, there really is no cluster score that
would come with the data. However, we provide an
implementation here so that you can score UniGene clusters
if you want to.
Returns : a number
Args : optionally, on set a number |
Title : get_members
Usage : Bio::ClusterI->get_members(($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 : |
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) |
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. |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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) |
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) |
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) |
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 |
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 |
Title : sequence_factory
Usage : $seqio->sequence_factory($seqfactory)
Function: Get/Set the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args : [optional] Bio::Factory::SequenceFactoryI |
Title : _annotation_value
Usage :
Function: Private method.
Example :
Returns : the value (a string)
Args : annotation key (a string)
on set, annotation value (a string) |
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 |
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 |
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
sub new
{
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;
$self->object_id($id) if $id;
$self->namespace($ns || 'UniGene');
$self->authority($auth || 'NCBI');
$self->version($v) if defined($v);
if( ! defined $seqfact ) {
$seqfact = new Bio::Seq::SeqFactory
(-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]/)) {
$species = $species_map{$1};
}
$self->species($species);
return $self; } | sub unigene_id
{ my ($obj,$value) = @_;
if( defined $value) {
$obj->{'unigene_id'} = $value;
}
return $obj->{'unigene_id'};} | sub title
{ my ($obj,$value) = @_;
if( defined $value) {
$obj->{'title'} = $value;
}
return $obj->{'title'};} | sub gene
{ my $self = shift;
return $self->_annotation_value('gene_name', @_);} | sub cytoband
{ my $self = shift;
return $self->_annotation_value('cyto_band', @_);} | sub mgi
{ my $self = shift;
my $acc;
if(@_) {
$self->_remove_dblink('dblink','MGI');
if($acc = shift) {
$self->_annotation_dblink('dblink','MGI',$acc);
}
} else {
($acc) = $self->_annotation_dblink('dblink','MGI');
}
return $acc;} | sub locuslink
{ my ($self,$ll) = @_;
if($ll) {
$self->_remove_dblink('dblink','LocusLink');
foreach my $acc (@$ll) {
$self->_annotation_dblink('dblink','LocusLink',$acc);
}
} else {
my @accs = $self->_annotation_dblink('dblink','LocusLink');
$ll = [@accs];
}
return $ll;} | sub gnm_terminus
{ my $self = shift;
return $self->_annotation_value('gnm_terminus', @_);} | sub scount
{ my ($obj,$value) = @_;
if( defined $value) {
$obj->{'scount'} = $value;
} elsif((! defined($obj->{'scount'})) && defined($obj->sequences())) {
$obj->{'scount'} = $obj->size();
}
return $obj->{'scount'};} | sub express
{ my $self = shift;
return $self->_annotation_value_ary('expressed',@_);} | sub chromosome
{ my $self = shift;
return $self->_annotation_value_ary('chromosome',@_);} | sub sts
{ my $self = shift;
return $self->_annotation_value_ary('sts',@_);} | sub txmap
{ my $self = shift;
return $self->_annotation_value_ary('txmap',@_);} | sub protsim
{ my $self = shift;
return $self->_annotation_value_ary('protsim',@_);} | sub sequences
{ my $self = shift;
return $self->{'members'} = shift if @_;
return $self->{'members'};} | 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'};} | sub display_id
{ return shift->unigene_id(@_); } | sub description
{ return shift->title(@_); } | sub size
{ my $self = shift;
return $self->scount(@_) unless defined($self->sequences());
my $n = scalar(@{$self->sequences()});
if(@_ && ($n != $_[0])) {
$self->throw("Cannot change cluster size using size() from $n to ".
$_[0]);
}
return $n;} | sub cluster_score
{ my $self = shift;
return $self->{'cluster_score'} = shift if @_;
return $self->{'cluster_score'};} | sub get_members
{ my $self = shift;
my $mems = $self->sequences() || [];
if(@$mems && (ref($mems->[0]) eq "HASH")) {
my @memlist = ();
while(my $seq = $self->next_seq()) {
push(@memlist, $seq);
}
$mems =\@ memlist;
$self->sequences($mems);
}
return @$mems;} | sub annotation
{ my $self = shift;
if(@_) {
return $self->{'annotation'} = shift;
} elsif(! exists($self->{'annotation'})) {
$self->{'annotation'} = Bio::Annotation::Collection->new();
}
return $self->{'annotation'};} | sub add_member
{ my ($self,@mems) = @_;
my $memlist = $self->{'members'} || [];
if(@$memlist && (ref($memlist->[0]) eq "HASH")) {
$memlist = [$self->get_members()];
}
push(@$memlist, @mems);
$self->sequences($memlist);
return 1;} | sub remove_members
{ my $self = shift;
my @mems = $self->get_members();
$self->sequences(undef);
return @mems;} | sub next_locuslink
{ my ($obj) = @_;
return $obj->_next_element("ll","locuslink");} | sub next_express
{ my ($obj) = @_;
return $obj->_next_element("express","express");} | sub next_chromosome
{ my ($obj) = @_;
return $obj->_next_element("chr","chromosome");} | sub next_protsim
{ my ($obj) = @_;
return $obj->_next_element("protsim","protsim");} | sub next_sts
{ my ($obj) = @_;
return $obj->_next_element("sts","sts");} | sub next_txmap
{ my ($obj) = @_;
return $obj->_next_element("txmap","txmap");} | sub _next_element
{ my ($self,$queuename,$meth) = @_;
$queuename = "_".$queuename."_queue";
if(! exists($self->{$queuename})) {
$self->{$queuename} = [@{$self->$meth() }];
}
my $queue = $self->{$queuename};
if(! @$queue) {
delete $self->{$queuename};
return undef;
}
return shift(@$queue);} | sub object_id
{ return shift->unigene_id(@_); } | sub version
{ my $self = shift;
return $self->{'version'} = shift if @_;
return $self->{'version'};} | sub authority
{ my $self = shift;
return $self->{'authority'} = shift if @_;
return $self->{'authority'};} | sub namespace
{ my $self = shift;
return $self->{'namespace'} = shift if @_;
return $self->{'namespace'};} | sub display_name
{ return shift->unigene_id(@_); } | sub next_seq
{ my ($obj) = @_;
if(! exists($obj->{'_seq_queue'})) {
$obj->{'_seq_queue'} = [@{$obj->sequences()}];
}
my $queue = $obj->{'_seq_queue'};
if(! @$queue) {
delete $obj->{'_seq_queue'};
return undef;
}
my $seq_h = shift(@$queue);
return $seq_h if(ref($seq_h) ne 'HASH');
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);
}
my $seqobj = $obj->sequence_factory->create(
-accession_number => $seq_h->{acc},
-pid => $seq_h->{pid},
-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(),
-species => $obj->species(),
-annotation => $ac
);
return $seqobj;} | sub sequence_factory
{ my ($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'};} | 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($ann && (! $val)) {
$val = $ann->value();
} elsif($val) {
if(! $ann) {
$ann = Bio::Annotation::SimpleValue->new(-tagname => $key);
$self->annotation->add_Annotation($ann);
}
$ann->value($val);
}
return $val;} | sub _annotation_value_ary
{ my ($self,$key,$arr) = @_;
my $ac = $self->annotation;
if($arr) {
$ac->remove_Annotations($key);
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 $arr;} | sub _annotation_dblink
{ my ($self,$key,$dbname,$acc,$version) = @_;
if($acc) {
my $ann = Bio::Annotation::DBLink->new(-tagname => $key,
-primary_id => $acc,
-database => $dbname,
-version => $version);
$self->annotation->add_Annotation($ann);
return 1;
} else {
my @anns = $self->annotation->get_Annotations($key);
if($dbname) {
@anns = grep { $_->database() eq $dbname; } @anns;
}
return map { $_->primary_id(); } @anns;
}} | sub _remove_dblink
{ my ($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;} | General documentation
| Implemented Interfaces | Top |
This class implementes the following interfaces.
Bio::Cluster::UniGeneI
This includes implementing Bio::ClusterI.
Bio::IdentifiableI
Bio::DescribableI
Bio::AnnotatableI
Bio::Factory::SequenceStreamI
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://bio.perl.org/MailList.html - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
| AUTHOR - Andrew Macgregor | Top |
Hilmar Lapp, hlapp at gmx.net
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
| Annotatable view at the object properties | Top |
| Implementation specific methods | Top |
These are mostly for adding/removing to array properties, and for
methods with special functionality.