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::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)