view release on metacpan or  search on metacpan

lib/Bio/ConnectDots/SimpleGraph.pm  view on Meta::CPAN

           means you can get from any node of the component to any
           other by following a path.  'Maximal' means that every node
           you can reach from the component is in the component.
 Args    : None
 Returns : ARRAY or ARRAY ref of SimpleGraphs
 Note    : The software caches the components once computed, so it's efficient
           to call this repeatedly.

 Title   : shortest_paths
 Usage   : my $paths=$graph->shortest_paths;
           while(my($endpoints,$path)=each %$paths) {
             my($start,$stop)=split($;,$endpoints);
             my @nodes_on_path=@$path;
             print "Path from $start to $stop: @$nodes_on_path\n";
           }
           -- OR --
           my ($paths,$distances)=$graph->shortest_paths(-want_distances=>1);
           while(my($endpoints,$path)=each %$paths) {
             my $distance=$distances->{$endpoints};
             my($start,$stop)=split($;,$endpoints);
             my @nodes_on_path=@$path;
             print "Path from $start to $stop, distance $distance: @$nodes_on_path\n";
           }
 Function: Compute shortest path between each pair of nodes.
 Args    : (optional)
           -max=>Maximum path length to compute
                 Paths longer than this are not found
           -want_distances=>Boolean. If true, distances are also returned
 Returns : HASH whose keys are pairs of nodes (encoded in the standard
           Perl manner as two strings joined by $;) and whose values
           are paths. Each path is an ARRAY ref of nodes starting at
           the first endpoint and ending at the second.

           The first endpoint is always lexically smaller (lt) than
           the second.

           If -want_distances is specified, the result is a pair of
           HASHes, one containing paths and the other containing
           distances.

 Title   : distances
 Usage   : my $distances=$graph->distances;
           while(my($endpoints,$distance)=each %$distances) {
             my($start,$stop)=split($;,$endpoints);
             print "Path from $start to $stop has distance $distance\n";
           }
           -- OR --
           my ($paths,$distances)=$graph->distances(-want_paths=>1);
           while(my($endpoints,$distance)=each %$distances) {
             my $path=$paths->{$endpoints};
             my($start,$stop)=split($;,$endpoints);
             my @nodes_on_path=@$path;
             print "Path from $start to $stop, distance $distance: @$nodes_on_path\n";
           }
 Function: Compute distance between each pair of nodes. This is the
           length of the shortest path
 Args    : (optional)
           -max=>Maximum path length to compute
                 Distances longer than this are not found
           -want_paths=>Boolean. If true, paths are also returned
 Returns : HASH whose keys are pairs of nodes (encoded in the standard
           Perl manner as two strings joined by $;) and whose values
           are distances.

           The first endpoint is always lexically smaller (lt) than
           the second.

           If -want_paths is specified, the result is a pair of
           HASHes, one containing paths and the other containing
           distances.

 Title   : connected_nodesets
 Usage   : my @nodesets=$graph->connected_nodesets;
           for my $nodeset (@nodesets) {
             my @nodes=@$nodeset;