Chris Mungall > go-perl-0.14 > GO::Model::GraphIterator;

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NAME ^

  GO::Model::GraphIterator;

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 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.

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