[Biojava-l] Getting features with the same Location

[Richard Holland]

Yes, the bioentry_id is private.

You could temporarily modify the BioEntry object in your local copy to
make the getId() method public, which would then give you access to
bioentry_id.

cheers,
Richard

Augusto Fernandes Vellozo wrote:
> Thanks Mark and Richard.
> 
> Yes Richard, I am using BIOSQL and Gabrielle said that she doesn't
> know a solution to the problem.
> Mark, if I use your suggestion, do I need to retrieve all features of
> the sequence and analyze each one?
> 
> I am thinking to use direct SQL query to retrieve the features id whit
> the same location start x of the sequence s and after to load each
> feature of this resultset to test the equals(location). With this
> filter, the quantity of the executions of equals(Location) will be
> reduced a lot. The problem is: I don't have the sequence bioentry_id
> to use in the direct SQL query. I have an object sequence but I don't
> have access to bioentry_id.
> 
> Thanks,
> 
> Augusto
> 
> 2008/12/11 Mark Schreiber <markjschreiber at gmail.com>:
>> You might also want to use the LocationTools class to determine if the
>> locations of the two features intersect or if one wholey contains
>> another.
>>
>> - Mark
>>
>> On Thu, Dec 11, 2008 at 6:55 PM, Richard Holland
>> <holland at eaglegenomics.com> wrote:
>>> Are you using BioSQL?
>>>
>>> If you are, take a look at the BioSQLFeatureFilter classes. These will
>>> construct a query which will only return the features you are
>>> specifically interested in.
>>>
>>> This bit of code should work once you've connected your BioJava instance
>>> to BioSQL (from an earlier post by Gabrielle Doan):
>>>
>>>       public FeatureHolder filterFeature(String name, int startpos, int
>>> endpos) {
>>>               RichLocation rl = new SimpleRichLocation(new
>>> SimplePosition(startpos),
>>>                               new SimplePosition(endpos), 0);
>>>               BioSQLFeatureFilter filter = new BioSQLFeatureFilter.And(
>>>                               new
>>> BioSQLFeatureFilter.BySequenceName(name),
>>>                               new
>>> BioSQLFeatureFilter.OverlapsRichLocation(rl));
>>>               return BioSQLRichSequenceDB.filter(filter);
>>>       }
>>>
>>> However, please note that Gabrielle reported a bug on the mailing list
>>> back in October with the above code. It's unclear whether or not it's
>>> yet been fixed as I can't find the entry in BugZilla.
>>>
>>> cheers,
>>> Richard
>>>
>>> Augusto Fernandes Vellozo wrote:
>>>> Hi everyone.
>>>>
>>>> I need to get all features of a sequence that are on the same location L.
>>>> I was thinking to do this getting all features of the sequence and
>>>> after executing the equals(L) for each one.
>>>> But, I have a lot of features in a sequence. I am trying to reduce the
>>>> resultset of features to test the equals, getting only the features
>>>> that start in the position L.getMin()
>>>>
>>>> Please, someone knows how can I do this?
>>>>
>>>> Thanks,
>>>>
>>> --
>>> Richard Holland, BSc MBCS
>>> Finance Director, Eagle Genomics Ltd
>>> M: +44 7500 438846 | E: holland at eaglegenomics.com
>>> http://www.eaglegenomics.com/
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
> 
> 
> 

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/