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.\" ========================================================================
.\"
.IX Title "GO::Model::GraphIterator 3pm"
.TH GO::Model::GraphIterator 3pm "2014-02-01" "perl v5.18.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
.Vb 1
\&  GO::Model::GraphIterator \- Graph iterator
.Ve
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  $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\en",
\&          "\-\-\-\-" x $depth,
\&          $reltype,
\&          $term\->name,
\&          $term\->public_acc,
\&          $depth;
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.SH "SEE ALSO"
.IX Header "SEE ALSO"
GO::Model::Graph
.PP
GO::Model::GraphNodeInstance
.SS "order"
.IX Subsection "order"
.Vb 3
\&  Usage   \- $graphiter\->order("breadth");
\&  Returns \- string
\&  Args    \- string
.Ve
.PP
gets/sets traversal order; breadth or depth; default is depth
.SS "direction"
.IX Subsection "direction"
.Vb 3
\&  Usage   \- $graphiter\->direction("up");
\&  Returns \- string
\&  Args    \- string
.Ve
.PP
gets/sets direction; default is \*(L"down\*(R"
.SS "compact"
.IX Subsection "compact"
.Vb 3
\&  Usage   \- $graphiter\->compact(1);
\&  Returns \- bool
\&  Args    \- bool
.Ve
.PP
set this if you dont want relationships to be traversed twice;
this gives a more compact tree representation of the graph
.SS "reltype_filter"
.IX Subsection "reltype_filter"
.Vb 3
\&  Usage   \- $graphiter\->reltype_filter(qw(is_a part_of))
\&  Returns \- array
\&  Args    \- array
.Ve
.PP
by default, all relationship types are treated as transitive, and will
be traversed by the iterator
.PP
sometimes you dont want to traverse all relations, even if they are
transitive. For example, when answering the query \*(L"find all genes
expressed in the embryo\*(R" you way want subtypes of embryo and parts of
the embryo but not things that develop_from the embryo.
.PP
For more details, see
<http://sourceforge.net/mailarchive/forum.php?thread_id=9448679&forum_id=43082>
.SS "reset_cursor"
.IX Subsection "reset_cursor"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.SS "next_node"
.IX Subsection "next_node"
.Vb 3
\&  Usage   \-
\&  Returns \- GO::Model::Term
\&  Args    \-
.Ve
.SS "next_node_instance"
.IX Subsection "next_node_instance"
.Vb 3
\&  Usage   \-
\&  Returns \- GO::Model::GraphNodeInstance
\&  Args    \-
.Ve
.SS "flatten"
.IX Subsection "flatten"
.Vb 3
\&  Usage   \-
\&  Returns \-
\&  Args    \-
.Ve
.SS "_sortby_pos_in_list"
.IX Subsection "_sortby_pos_in_list"
Careful, this sort function work on Term objects, not GraphNodeInstance
objects.  Comparison is done by the name of the term.