/ 
bioperl-1.4
/ Bio::Cluster::UniGene

NAME

Bio::Cluster::UniGene - UniGene object

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

Implemented Interfaces

This class implementes the following interfaces.

Bio::Cluster::UniGeneI

This includes implementing Bio::ClusterI.

Bio::IdentifiableI
Bio::DescribableI
Bio::AnnotatableI
Bio::Factory::SequenceStreamI

FEEDBACK

Mailing Lists

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

Reporting Bugs

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

Email andrew@anatomy.otago.ac.nz

CONTRIBUTORS

Hilmar Lapp, hlapp at gmx.net

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".

new

Title   : new
Usage   : used by ClusterIO
Returns : a new Bio::Cluster::Unigene object

Bio::Cluster::UniGeneI methods

unigene_id

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   : 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

gene

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

cytoband

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

mgi

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

gnm_terminus

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

scount

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

express

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

chromosome

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

sts

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

txmap

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

protsim

 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

sequences

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

species

Title   : species
Usage   : $obj->species($newval)
Function: Get/set the species object for this Unigene cluster.
Example : 
Returns : value of species (a L<Bio::Species> object)
Args    : on set, new value (a L<Bio::Species> object or 
          the binomial name, or undef, optional)

Bio::ClusterI methods

display_id

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

Title   : description
Usage   : Bio::ClusterI->description("POLYUBIQUITIN")
Function: get/set for the consensus description of the cluster

          This is aliased to title().

Returns : the description string 
Args    : Optional the description string

size

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_score

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_members

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    :

Annotatable view at the object properties

annotation

Title   : annotation
Usage   : $obj->annotation($newval)
Function: Get/set the L<Bio::AnnotationCollectionI> object for
          this UniGene cluster.

          Many attributes of this class are actually stored within
          the annotation collection object as L<Bio::AnnotationI>
          compliant objects, so you can conveniently access them
          through the same interface as you would e.g. access
          L<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 L<Bio::AnnotationCollectionI> compliant object
Args    : on set, new value (a L<Bio::AnnotationCollectionI> 
          compliant object or undef, optional)

Implementation specific methods

These are mostly for adding/removing to array properties, and for
methods with special functionality.

add_member

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_members

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

next_express

 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_chromosome

 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_protsim

 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_sts

 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_txmap

 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

Bio::IdentifiableI methods

object_id

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

version

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)

authority

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)

namespace

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)

Bio::DescribableI methods

display_name

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

description()

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

Bio::Factory::SequenceStreamI methods

next_seq

 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_factory

Title   : sequence_factory
Usage   : $seqio->sequence_factory($seqfactory)
Function: Get/Set the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args    : [optional] Bio::Factory::SequenceFactoryI

Private methods

_annotation_value

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_ary

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_dblink

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_dblink

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)