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GO::Model::GraphIterator

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\n",
"----" 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 don’t 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 don’t 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.

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