go::utils(3pm) [debian man page]
GO::Utils(3pm) User Contributed Perl Documentation GO::Utils(3pm) NAME
GO::Utils - utilities for GO modules rearrange() Usage : n/a Function : Rearranges named parameters to requested order. Returns : @params - an array of parameters in the requested order. Argument : $order : a reference to an array which describes the desired order of the named parameters. @param : an array of parameters, either as a list (in which case the function simply returns the list), or as an associative array (in which case the function sorts the values according to @{$order} and returns that new array. Exceptions : carps if a non-recognised parameter is sent get_param() Usage : get_param('name',(-att1=>'ben',-name=>'the_name')) Function : Fetches a named parameter. Returns : The value of the requested parameter. Argument : $name : The name of the the parameter desired @param : an array of parameters, as an associative array Exceptions : carps if a non-recognised parameter is sent Based on rearrange(), which is originally from CGI.pm by Lincoln Stein and BioPerl by Richard Resnick. See rearrange() for details. remove_duplicates remove duplicate items from an array usage: remove_duplicates(@arr) affects the array passed in, and returns the modified array merge_hashes joins two hashes together usage: merge_hashes(\%h1, \%h2); %h1 will now contain the key/val pairs of %h2 as well. if there are key conflicts, %h2 values will take precedence. get_method_ref returns a pointer to a particular objects method e.g. my $length_f = get_method_ref($seq, 'length'); $len = &$length_f(); pset2hash Usage - my $h = pset2hash([{name=>"id", value=>"56"}, {name=>"name", value=>"jim"}]); Returns - hashref Args - arrayref of name/value keyed hashrefs spell_greek takes a word as a parameter and spells out any greek symbols encoded within (eg s/&agr;/alpha/g) check_obj_graph Usage - Returns - true if cycle detected Args - any object perl v5.14.2 2013-02-07 GO::Utils(3pm)
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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)