I know that this is really Java language topic, but since parsing biological
data formats is to rife with regular expression applications, I'm curious what
the experience is among the Biojava people with the use of regular expressions
in Java.
They (at least as in java.util.regex) have been reported to me as performing
much slower (by several orders of magnitude) than the regex implementation in
Perl, and some simple benchmarking tests seem to bear that out. Even after
scrutinizing the benchmark and finding nothing obvious, I'm still skeptical as
to why this would be the case - naively I would have assumed that the
underlying runtime library is implemented in C in both cases. But perhaps this
is not true?
Any experience people have made here speed-wise (or tricks or things not to do
for Java regex's) would be appreciated.
-hilmar
--
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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