[Biojava-l] Genbank feature parsing performance

[Khalil El Mazouari]

Hi,

I am developing an app where features are extracted from a large genbank file, and processed: multiple alignment, annotation....

The feature extraction is a real bottleneck in my app. It consumes 87% of total execution time. 

Feature extraction is done via:

FeatureFilter ff = new FeatureFilter.ByAnnotation(key, value);
FeatureHolder fh = richSequence.filter(ff);
Feature feat = fh.features().next();
...

Any suggestion on how to improve the performance of features extraction is welcome.

Thanks,

khalil