Bio::Cluster::UniGeneI - abstract interface of UniGene object # This is the general interface for a UniGene cluster representation in Bioperl. You cannot use this module directly, use an implementation instead. You can create UniGene cluster objects yourself by instantiating Bio::Cluster::UniGene. If you read UniGene clusters from a ClusterIO parser, you will get objects implementing this interface, most likely instances of said UniGene class. Bio::Cluster::UniGeneI inherits from Bio::ClusterI, so you can use it wherever a cluster object is expected. #

Mailing Lists
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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/ Email andrew@anatomy.otago.ac.nz The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".

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

locuslink
Title : locuslink Usage : locuslink(); Function: Returns or stores a reference to an array containing locuslink data. This should really only be used by ClusterIO, not directly 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. This should really only be used by ClusterIO, not directly 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 This should really only be used by ClusterIO, not directly 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 This should really only be used by ClusterIO, not directly 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

sequence
Title : sequence Usage : sequence(); Function: Returns or stores a reference to an array containing sequence data This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference

species
Title : species Usage : $obj->species($newval) Function: Get the species object for this Unigene cluster. Example : Returns : value of species (a L<Bio::Species> object) Args :

display_id
Title : display_id Usage : Function: Get/set the display name or identifier for the cluster 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 Returns : the description string Args : Optional the description string

size
Title : size Usage : Bio::ClusterI->size(); Function: get/set for the size of the family, calculated from the number of members Returns : the size of the family 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. Returns : a number

get_members
Title : get_members Usage : Bio::ClusterI->get_members(($seq1, $seq2)); Function: retrieve the members of the family by some criteria, for example : $cluster->get_members(-species => 'homo sapiens'); Will return all members if no criteria are provided. Returns : the array of members Args :