go::model::association(3pm) [debian man page]

GO::Model::Association(3pm)				User Contributed Perl Documentation			       GO::Model::Association(3pm)

NAME

	 GO::Model::Association - association between a GO term and a gene product

SYNOPSIS

	 # print all gene products associated with a GO::Model::Term
	 my $assoc_l = $term->association_list;
	 foreach my $assoc (@$assoc_l) {
	   printf "gene product:%s %s %s (evidence: %s)
",
	     $assoc->gene_product->symbol,
	     $assoc->is_not ? "IS NOT" : "IS",
	     $term->name,
	     map {$_->code} @{$assoc->evidence_list};
	 }

DESCRIPTION

       Represents an association between a GO term (GO::Model::Term) and a gene product (GO::Model::GeneProduct)

   go_public_acc
	 Usage	 -
	 Returns -
	 Args	 -

   add_evidence
	 Usage	 - $assoc->add_evidence($my_evid);
	 Returns -
	 Args	 - GO::Model::Evidence

   evidence_list
	 Usage	 - my $ev_l = $assoc->evidence_list;
	 Returns -
	 Args	 -

       gets/sets arrayref of GO::Model::Evidence

   evidence_as_str
	 Usage	 - print $assoc->evidence_as_str
	 Usage	 - print $assoc->evidence_as_str(1); #verbose
	 Returns -
	 Args	 - verbose

       concatenates evcodes together, for display

   has_evcode
	 Usage	 - if $assoc->has_evcode("IEA");
	 Returns - boolean
	 Args	 - evcode [string]

   remove_evcode
	 Usage	 - $assoc->remove_evcode("IEA");
	 Returns -
	 Args	 - evcode [string]

       removes all evidence of the specified type from the association; useful for filtering

   evidence_score
	 Usage	 - my $score = $assoc->evidence_score
	 Returns - 0 <= float <= 1
	 Args	 -

       returns a score for the association based on the evidence;

       This is an EXPERIMENTAL method; it may be removed in future versions.

       The evidence fields can be thought of in a loose hierachy:

       TAS
	  IDA
	     IMP/IGI/IPI
			ISS
			   NAS

       see http://www.geneontology.org/GO.evidence.html

   gene_product
	 Usage	 - my $gp = $assoc->gene_product
	 Returns -
	 Args	 -

       gets sets GO::Model::GeneProduct

   assigned_by
	 Usage	 -
	 Returns -
	 Args	 -

   is_not
	 Usage	 -
	 Returns -
	 Args	 -

       gets/sets boolean representing whether this relationship is negated

   assocdate
	 Usage	 -
	 Returns -
	 Args	 -

   assocdate
	 Usage	 -
	 Returns -
	 Args	 -

       gets/sets integer representing the date of the association (YYYYMMDD format)

   role_group
	 Usage	 -
	 Returns -
	 Args	 -

       gets/sets integer to indicate which associations go together

perl v5.14.2							    2013-02-07					       GO::Model::Association(3pm)

Bio::Structure::Model(3pm)				User Contributed Perl Documentation				Bio::Structure::Model(3pm)

NAME

       Bio::Structure::Model - Bioperl structure Object, describes a Model

SYNOPSIS

	 #add synopsis here

DESCRIPTION

       This object stores a Bio::Structure::Chain

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://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       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 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 the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Kris Boulez
       Email kris.boulez@algonomics.com

APPENDIX

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

   new()
	Title	: new()
	Usage	: $struc = Bio::Structure::Model->new(
						  -id  => 'human_id',
						  );

	Function: Returns a new Bio::Structure::Model object from basic
	       constructors. Probably most called from Bio::Structure::IO.
	Returns : a new Bio::Structure::Model object

   chain()
	Title	: chain
	Usage	:
	Function: will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   add_chain()
	Title	: add_chain
	Usage	:
	Function:  will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   entry()
	Title	: entry
	Usage	:
	Function:  will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   id()
	Title	: id
	Usage	: $model->id("model 5")
	Function: Gets/sets the ID for this model
	Returns : the ID
	Args	: the ID

   residue()
	Title	: residue
	Usage	:
	Function:  will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   add_residue()
	Title	: add_residue
	Usage	:
	Function:  will eventually allow parent/child navigation not via an Entry object
	Returns :
	Args	:

   _remove_chains()
	Title	: _remove_chains
	Usage	:
	Function: Removes the chains attached to a Model. Tells the chains they
	       don't belong to this Model any more
	Returns :
	Args	:

   _remove_entry()
	Title	: _remove_entry
	Usage	:
	Function: Removes the Entry this Model is atttached to.
	Returns :
	Args	:

   _create_default_chain()
	Title	: _create_default_chain
	Usage	:
	Function: Creates a default Chain for this Model. Typical situation
	       in an X-ray structure where there is only one chain
	Returns :
	Args	:

   _grandparent()
	Title	: _grandparent
	Usage	:
	Function: get/set a symbolic reference to our grandparent
	Returns :
	Args	:

perl v5.14.2							    2012-03-02						Bio::Structure::Model(3pm)