Re: [Treebase-devel] viz problem with trees for S11267

[William P. <wil...@ya...>]

Whoops... forgot to reply to <TreeBASE Devel>. 

At any rate, I just noticed that someone form the Czech Republic has uploaded >20 files, each with > 60,000 sequences, this might be causing java heap size issues. 

bp



On Apr 14, 2011, at 8:39 AM, William Piel wrote:

> Hi Rod,
> 
> Some performance measures should have improved since your earlier efforts with the API. Morphological datasets, for example, should download much faster -- in part seeing as the database has shrunk from ~200GB to 3GB in size.  
> 
> But of course you're right -- the API needs to be much more efficient, e.g. refactored so that the CQL translates more directly into HQL instead of just hitching in to our web SearchController. 
> 
> Regarding the user interface usability -- as you know, this is an unfunded open source project -- so you're very welcome to make improvements ! 
> 
> bp
> 
> 
> On Apr 14, 2011, at 7:28 AM, Roderic Page wrote:
> 
>> TreeBASE  performance has nothing to do with me folks, I pretty much gave up trying to download data from it a few weeks back. Someone really, really needs to rethink the way TreeBASE works, because it's virtually unusable.
>> 
>> Regards
>> 
>> Rod
>> 
>> On 14 Apr 2011, at 04:20, William Piel wrote:
>> 
>>> 
>>> On Apr 13, 2011, at 9:36 PM, Hilmar Lapp wrote:
>>> 
>>>> The trees in S11267 seem to silently fail to render in PhyloWidget.  
>>>> All I get is a single dot. At least try the first three:
>>>> 
>>>> http://www.treebase.org/treebase-web/search/study/trees.html?id=11267
>>>> 
>>>> Is this a temporary glitch, a problem with the reconstructed file, or  
>>>> something else? Should I best file this as a bug in the bug tracker?
>>>> 
>>>> 	-hilmar
>>>> 
>>> 
>>> Thanks for the alert. This is actually a bug in PhyloWidget -- if the word "tree" appears in the title of the tree block, PhyloWidget confuses this word with the TREE command, and so goofs up the parsing. 
>>> 
>>> I have removed the word "tree" from the tree block, so it works now. 
>>> 
>>> However, you might need to refresh the PhyloWidget window after loading to get the tree to pull through -- TreeBASE feels quite slow lately; our API must be getting hit by  someone (Rod?). 
>>> 
>>> bp
>>> 
>>> 
>>> 
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