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

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

NAME

	 GO::Model::GraphIterator - wraps GO::Model::GraphIterator

SYNOPSIS

DESCRIPTION

       This is a hack.	It wraps GO::Model::GraphIterator and provides a tree like iteration, rather than a graph-like iteration.

       This is done by giving TreeIterator a template array.

       The array looks like this :

       [ [3674, 'isa', 3673], [9277, 'isa', 5618] ]

       3674 is selected iff it is the child of 3673.  9277 is selected iff it is the child of 5618.

   order
	 Usage	 - $graphiter->order("breadth");
	 Returns - string
	 Args	 - string

       gets/sets traversal order; breadth or depth; default is depth

   direction
	 Usage	 - $graphiter->direction("up");
	 Returns - string
	 Args	 - string

       gets/sets direction; default is "down"

   reset_cursor
	 Usage	 -
	 Returns - GO::Model::Term
	 Args	 -

   next_node
	 Usage	 -
	 Returns - GO::Model::Term
	 Args	 -

   set_bootstrap_mode
	 Usage	 -
	 Returns -
	 Args	 -

   get_bootstrap_mode
	 Usage	 -
	 Returns -
	 Args	 -

   get_current_path
	 Usage	 -
	 Returns - array ref
	 Args	 - none

   next_node_instance
	 Usage	 -
	 Returns - GO::Model::GraphNodeInstance
	 Args	 -

perl v5.14.2							    2013-02-07					      GO::Model::TreeIterator(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)