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

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

NAME

	 GO::Model::Root - base class for all GO::Model objects

DESCRIPTION

       base class for all GO::Model objects

Constructors
   new
       Constructor: Basically just calls _initialize().  Most subclasses should not need to override new, but instead should override
       _initialize().

       If _initialize() fails , the procedure will die

       WARNING: This procedure will die if initialization is unsuccessful.  Use an eval statement to catch such exceptions.

   obj_factory
	 Usage	 - $obj->obj_factory->create_new_term_object($h);
	 Alias	 - apph
	 Returns - L<GO::ObjFactory>
	 Args	 - none

   sprint_self
       Prints out a description of the object to a string.

   dump
       dumps the object (can be read back in with eval)

   namespace
	 Usage	 - print $term->namespace();	 # getting the type
	 Usage	 - $term->namespace("molecular_function"); # setting the type
	 Alias	 - type
	 Alias	 - term_type
	 Alias	 - category
	 Alias	 - ontology
	 Returns - string representing type
	 Args	 - string represnting type [optional]

       The OBO namespace for the GO::Model::Term or GO::Model::Relationship

   _cleanup
       Called at object destruction time.  Should be overridden to perform cleanup tasks.

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

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)