[Biojava-l] Different implementation of Sequence?

[Y D Sun]

Hi,

It seems that the implmentation for a sequence that is read from a plain
text file (e.g. Embl file) or from a BioSQL database is different.

I apply a feature filter to a sequence seq like:

            //make a Filter for "CDS" types
            FeatureFilter ff = new FeatureFilter.ByType("CDS");

            //get the filtered Features
            FeatureHolder fh = seq.filter(ff);

The feature filtering takes longer time for a sequence from database. In
my experiment, for example,

If seq is read from an Embl file, the time cost of seq.filter(ff) is 54
ms;
If the same seq is read from a BioSQL database, the time is 51518 ms (as
high as 1000 times).

The latter also requires more memory space in execution.

Could anybody give some justification for this phenomenon?

Thanks

George