Re: [Treebase-devel] Determining implicit root

[Hilmar L. <hl...@ne...>]

Yes, sorry for the noise. I realized that I was looking at an old revision only after I had sent the email. iPad isn't perfect for this ...

-hilmar

Sent with a tap.

On May 28, 2011, at 12:17 PM, Rutger Vos <R....@re...> wrote:

> Hi Hilmar,
> 
> you note that you are looking at a javascript snippet for determining
> the root in a nexml tree in preparation for displaying it in
> jsPhyloSVG, right?
> 
> Anyway, the following *doesn't* work, targetCount for the root should
> be 0 or possibly 1 in the case where a rootedge is an element in the
> nexEdges array. The head revision shows this done correctly.
> 
> I was trying to get jsPhyloSVG to play nice and this was just one of
> many things that weren't working properly so this ended up being
> committed in that revision without actually working
> 
> Rutger
> 
> On Sat, May 28, 2011 at 4:43 PM, Hilmar Lapp <hl...@dr...> wrote:
>> Rutger -
>> 
>> I'm curious and am probably missing something and therefore don't fully follow why the below works. Would you mind explaining? By edges pointing into a node, do you mean incoming (from ancestor) or outgoing (to descendant) edges? It sounds like outgoing (or otherwise there wouldn't be two, right), but why does NeXML then require a node with one outgoing edge at the root of the tree, artificial or not? Or do you mean outgoing plus incoming?
>> 
>> So I'm obviously missing something, but can you point me to what it is?
>> 
>> -hilmar
>> 
>> Sent with a tap.
>> 
>> On May 19, 2011, at 9:00 AM, rv...@us... wrote:
>> 
>>> Revision: 873
>>>          http://treebase.svn.sourceforge.net/treebase/?rev=873&view=rev
>>> Author:   rvos
>>> Date:     2011-05-19 13:00:28 +0000 (Thu, 19 May 2011)
>>> 
>>> Log Message:
>>> -----------
>>> Added additional loop to identify the root node based on the implicit topology (instead of by looking for the @root attribute).
>>> 
>>> Modified Paths:
>>> --------------
>>>    trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
>>> 
>>> Modified: trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
>>> ===================================================================
>>> --- trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js    2011-05-19 12:57:49 UTC (rev 872)
>>> +++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js    2011-05-19 13:00:28 UTC (rev 873)
>>> @@ -761,6 +761,27 @@
>>>            }
>>>        }
>>> 
>>> +        // RAV: the root attribute is used to indicate whether an implicitly rooted
>>> +        // topology should, from a biological p.o.v., be considered as such. However,
>>> +        // valid NeXML tree structures are always rooted, even if they don't have
>>> +        // the root attribute, in the sense that there's always going to be one node
>>> +        // that doesn't have two edges pointing into it. It seems to me that we can
>>> +        // still render these trees, we just have to find which node is the one that
>>> +        // doesn't have two edges pointing in. This loop does that.
>>> +        if (!root){
>>> +            for(i = 0; i < nexNodes.length; i++) {
>>> +                var targetCount = 0;
>>> +                for(j = 0; j < nexEdges.length; j++) {
>>> +                    if(nexEdges[j].target == nexNodes[i].id) {
>>> +                        targetCount++;
>>> +                    }
>>> +                }
>>> +                if ( targetCount < 2 ) {
>>> +                    root = nexNodes[i];
>>> +                }
>>> +            }
>>> +        }
>>> +
>>>        if(root){
>>>            root = recursiveParse(root);
>>> 
>>> 
>>> 
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> 
> 
> 
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading, RG6 6BX, United Kingdom
> Tel: +44 (0) 118 378 7535
> http://rutgervos.blogspot.com
> 
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