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

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

NAME

	 GO::Model::GeneProduct - gene product in a particular species

DESCRIPTION

       represents a gene product in a particular species (this will effectively always be refered to implicitly by the gene symbol even though a
       gene may have >1 product)

   acc
	 Usage	 -
	 Returns -
	 Args	 -

   symbol
	 Usage	 -
	 Returns -
	 Args	 -

   type
	 Usage	 -
	 Returns -
	 Args	 -

   full_name
	 Usage	 -
	 Returns -
	 Args	 -

   as_str
	 Usage	 -
	 Returns -
	 Args	 -

   add_synonym
   synonym_list
       accessor: gets/set list of synonyms [array reference]

   speciesdb
	 Usage	 -
	 Returns -
	 Args	 -

   add_seq
	 Usage	 -
	 Returns -
	 Args	 - GO::Model::Seq

   seq_list
	 Usage	 -
	 Returns - GO::Model::Seq listref
	 Args	 -

   seq
	 Usage	 -
	 Returns - GO::Model::Seq
	 Args	 -

       returns representative sequence object for this product

   properties
	 Usage	 -
	 Returns - hashref
	 Args	 - hashref

   set_property
	 Usage	 - $sf->set_property("wibble", "on");
	 Returns -
	 Args	 - property key, property scalar

       note: the property is assumed to be multivalued, therefore
	 $sf->set_property($k, $scalar) will add to the array, and
	 $sf->set_property($k, $arrayref) will set the array

   get_property
	 Usage	 -
	 Returns - first element of the property
	 Args	 - property key

   get_property_list
	 Usage	 -
	 Returns - the property arrayref
	 Args	 - property key

   to_fasta
	 Usage	 -
	 Returns -
	 Args	 -

       returns the longest seq by default

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

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

NAME

	 GO::Model::GraphIterator - Graph iterator

SYNOPSIS

	 $it = $graph->create_iterator;
	 # returns a GO::Model::GraphIterator object

	 while (my $ni = $it->next_node_instance) {
	   $depth = $ni->depth;
	   $term = $ni->term;
	   $reltype = $ni->parent_rel->type;
	   printf
	     "%s %8s Term = %s (%s)  // depth=%d
",
		 "----" x $depth,
		 $reltype,
		 $term->name,
		 $term->public_acc,
		 $depth;
	 }

DESCRIPTION

SEE ALSO

       GO::Model::Graph

       GO::Model::GraphNodeInstance

   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"

   compact
	 Usage	 - $graphiter->compact(1);
	 Returns - bool
	 Args	 - bool

       set this if you dont want relationships to be traversed twice; this gives a more compact tree representation of the graph

   reltype_filter
	 Usage	 - $graphiter->reltype_filter(qw(is_a part_of))
	 Returns - array
	 Args	 - array

       by default, all relationship types are treated as transitive, and will be traversed by the iterator

       sometimes you dont want to traverse all relations, even if they are transitive. For example, when answering the query "find all genes
       expressed in the embryo" you way want subtypes of embryo and parts of the embryo but not things that develop_from the embryo.

       For more details, see <http://sourceforge.net/mailarchive/forum.php?thread_id=9448679&forum_id=43082>

   reset_cursor
	 Usage	 -
	 Returns -
	 Args	 -

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

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

   flatten
	 Usage	 -
	 Returns -
	 Args	 -

   _sortby_pos_in_list
       Careful, this sort function work on Term objects, not GraphNodeInstance objects.  Comparison is done by the name of the term.

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