[Biojava-dev] Jronn ModelLoader resource problem

[P. Troshin]

Hmm, time to sleep, I meant to say I am guessing...

Cheers,
P


On 10 May 2012 00:52, P. Troshin <to.petr at gmail.com> wrote:

> Steve,
>
> I am guess, you wanted the following change:
>
> final BufferedReader bfr = new BufferedReader(
>                     new InputStreamReader(
>                             ModelLoader.class.getResourceAsStream(String
>                                     .format("model%d.rec", i))));
>
> Note the lack of / before the model.That seems to work fine.
> Does this work for you?
>
> Thanks,
> Peter
>
>
>
> On 10 May 2012 00:39, P. Troshin <to.petr at gmail.com> wrote:
>
>> Hi Steve,
>>
>> I am glad to hear that you find the predictor useful in your work.
>> However, I am afraid we may not be able to apply your patch as it breaks
>> the executable Jronn jar, it seems like the models cannot be loaded from
>> within the Jar file when your patch is applied. Could you tell us a bit
>> more about your setup? Why you cannot load the models with the old method?
>>
>> Thanks,
>> Peter
>>
>>
>>
>> On 9 May 2012 00:31, Steve Darnell <darnells at dnastar.com> wrote:
>>
>>> Greetings,
>>>
>>> I am having problems with loading resources for the Jronn (protein
>>> disorder) ModelLoader. With my usage, my program cannot locate the
>>> modelN.rec associated with the biojava3-protein-disorder module. I know
>>> that my program can locate other BioJava resources, such as the Blosum65
>>> matrix in the biojava3-alignment module used by the SeqRes2AtomAligner
>>> class.
>>>
>>> I noticed that ModelLoader.loadModels() uses a different coding pattern
>>> for getting a resource as a stream than other areas of BioJava.
>>> ModelLoader.loadModels() uses ClassLoader.getSystemResourceAsStream while
>>> SubstitutionMartixHelper.getReader uses
>>> $BIOJAVA_CLASS.class.getResourceAsStream().
>>>
>>> The following change to ModelLoader.java (line 163) works in my use case:
>>>
>>> > Original
>>>
>>>            final BufferedReader bfr = new BufferedReader(
>>>                new
>>> InputStreamReader(ClassLoader.getSystemResourceAsStream(
>>>                            "model" + i + ".rec"),
>>>                            "ISO-8859-1"));
>>>
>>> < Patch
>>>
>>>            final BufferedReader bfr = new BufferedReader(
>>>                new
>>> InputStreamReader(ModelLoader.class.getResourceAsStream(
>>>                                String.format("/model%d.rec", i))
>>>                    ));
>>>
>>> It appears that using the non-system resource method in the patch code
>>> searches for resources in more locations that the system resource method in
>>> the original code (
>>> http://docs.oracle.com/javase/6/docs/technotes/guides/lang/resources.html).
>>> The existing Jronn unit test for continues to work with the patch without
>>> modification.
>>>
>>> I am asking for the ModelLoader class in org.biojava3.ronn (from the
>>> biojava3-protein-disorder module) to be modified as described before the
>>> next BioJava release, making the code more robust and more consistent with
>>> existing BioJava coding patterns. I would be happy to address any questions
>>> or comments.
>>>
>>> Best regards,
>>> Steve
>>>
>>> --
>>> Steve Darnell
>>> DNASTAR, Inc.
>>> Madison, WI USA
>>>
>>>
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>
>>
>