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

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

NAME

	 GO::Model::Xref - cross reference to an external database

SYNOPSIS

	 my $xrefs = $term->dbxref_list();
	 foreach my $xref (@$xrefs) P
	   printf "Term %s has an xref %s:%s
",
		   $term->name, $xref->xref_key, $xref->dbname;
	 }

DESCRIPTION

       represents a cross reference to an external database. an Xref is made up of a key (ie the accession number, or whatever the value of the
       unique field being keyed off of is) and a database name. this should theorerically be enough to uniquely identify any databased entity.

NOTES

       Like all the GO::Model::* classes, this uses accessor methods to get or set the attributes. by using the accessor method without any
       arguments gets the value of the attribute. if you pass in an argument, then the attribuet will be set according to that argument.

       for instance

	 # this sets the value of the attribute
	 $my_object->attribute_name("my value");

	 # this gets the value of the attribute
	 $my_value = $my_object->attribute_name();

   xref_key
	 Alias	 - acc
	 Alias	 - accession
	 Usage	 -
	 Returns -
	 Args	 -

	accessor: gets/sets the key/id of the cross reference

   xref_keytype
	 Usage	 -
	 Returns -
	 Args	 -

	accessor: gets/sets the key/id type of the cross reference

   as_str
	 Usage	 -
	 Returns -
	 Args	 -

   xref_dbname
	 Alias	 - dbname
	 Usage	 -
	 Returns -
	 Args	 -

	accessor: gets/sets the database name of the cross reference

       must be a valid database name

   xref_desc
	 Alias	 - name
	 Usage	 -
	 Returns -
	 Args	 -

	accessor: gets/sets the description of the accession no

       useful for interpro

   to_xml
	 Usage	 - print $xref->to_xml()
	 Returns - string
	 Args	 - indent [integer]

       XML representation; you probably shouldnt call this directly, this will be called by entities that own xrefs

perl v5.14.2							    2013-02-07						      GO::Model::Xref(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)