| Bio::Cluster::UniGeneI(3pm) | User Contributed Perl Documentation | Bio::Cluster::UniGeneI(3pm) |
Bio::Cluster::UniGeneI - abstract interface of UniGene object
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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.
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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.
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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.
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://github.com/bioperl/bioperl-live/issues
Email andrew at cbbc.murdoch.edu.au
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".
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.
This should really only be used by ClusterIO, not directly
Returns : An array reference
Args : None or an array reference
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
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
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.
This should really only be used by ClusterIO, not directly
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
This should really only be used by ClusterIO, not directly
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
This should really only be used by ClusterIO, not directly
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 : 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
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 :
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)
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
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 :
Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number
Title : get_members
Usage : Bio::ClusterI->get_members(($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 :
| 2018-10-27 | perl v5.26.2 |