[BioRuby] Bio::Tree#children IndexError when called on a root node which does not have children.

[Diana Jaunzeikare]

Thanks for explanation, this makes sense now.

Diana

On Sun, Jul 12, 2009 at 4:46 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi Diana,
>
> On Sat, 11 Jul 2009 22:18:12 -0400
> Diana Jaunzeikare <rozziite at gmail.com> wrote:
>
> > Hi all,
> >
> > While i was writing parser for Phyloxml I discovered such behavior in
> > Bio::Tree class.
> >
> > Bio::Tree#children method gives IndexError if it is called on a root node
> > which does not have children.
> >
> > irb(main):002:0> tree = Bio::Tree.new
> > => #<Bio::Tree:0xb7d759e4 @root=nil, @pathway=#<Bio::Pathway:0xb7c490e8
> > @graph={}, @relations=[], @label={}, @undirected=true, @index={}>,
> > @options={}>
> >  irb(main):004:0> node = Bio::Tree::Node.new
> > => (Node:b7c43f80)
> > irb(main):005:0> node.name = "node1"
> > => "node1"
> > irb(main):006:0> tree.root = node
> >  => (Node:"node1")
> > irb(main):007:0> tree.children(tree.root)
> > IndexError: node1 not found
> >     from /usr/local/lib/site_ruby/1.8/bio/tree.rb:591:in `path'
> >     from /usr/local/lib/site_ruby/1.8/bio/tree.rb:640:in `children'
> >      from (irb):7
> > irb(main):008:0>
>
> The error shows that "tree.root" does not exist in the tree.
>
> Currently, Bio::Tree#root=(node) does not check whether
> the specified node exists in the tree or not, and it changes
> only the internal pointer to the root. In addition, it does
> not modify the tree except the pointer to the root.
>
> In this case, the node should be added to the tree.
>
> Before "tree.root = node" or "tree.children(tree.root)",
>    tree.add_node(node)
> is needed.
>
> Why the latter case works is that Bio::Tree#add_edge
> automatically adds nodes if the nodes do not exist in the tree.
>
> >
> >
> > If the children method is called on other than root node (which does not
> > have children), then it correctly gives empty array:
> >
> > irb(main):008:0> node2 = Bio::Tree::Node.new
> > => (Node:b7c3b088)
> > irb(main):009:0> node2.name = "node2"
> > => "node2"
> > irb(main):010:0> tree.add_node(node2)
> > => #<Bio::Tree:0xb7d759e4 @root=(Node:"node1"),
> > @pathway=#<Bio::Pathway:0xb7c490e8 @graph={(Node:"node2")=>{}},
> > @relations=[], @label={}, @undirected=true, @index={}>, @options={}>
> > irb(main):011:0> tree.add_edge(tree.root, node2)
> > => <Edge distance=nil>
> > irb(main):012:0> tree.children(node2)
> > => []
> > irb(main):013:0>
> >
> > If the root node has children, then everything is fine:
> >
> >  irb(main):013:0> tree.children(tree.root)
> > => [(Node:"node2")]
> >
> >
> > Diana
> >
>
>
> --
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>