Re: [MLUG] coding languages used in genetics

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> (SAS)  Yes.  It is really good for parsing text files in all kinds of
> ways.  We have also been using it to locate sequences in data files.

I was going to say that, as Perl's regular expression language/engine is second
to none. Other languages that have ripped off Perl's regex engine actually only
have an implementation of the "classic" regexes, not the extended syntaxes.
(Such as some of the positive and negative lookahead and lookbehind features)

And of course, they don't have the /e modifier. :=)

Damian Conway uses DNA sequences and proteins and implements transcription
processes in an elegant Object Oriented way, completely discrediting the myth
that Perl isn't an OO language. That's just because most of the Perl codebase
(CPAN) isn't by people that wrote OO code. I'm convinced (by Damian) that 
Perl's OO implementation is actually superior and more flexible to other OO 
environments.

Things like deterministic destructors and multiple inheritance are quite
important, it turns out. Java, for example, has to jump through hoops to do some
of these common OO features. Except what in the Perl world we call "throwaway
one-liners", Java programmers find themselves implementing the same workarounds
to the limitations of their language and libraries so often, that they call them
"patterns".

(Lack of) Closures ==> "inner classes"
Double-dispatch/callback => "Visitor Pattern"
"interpreted" => Reflection / Class Loaders / Bytecode enhancement
"dynamic method dispatch" => Reflection / Class Loaders / Bytecode enhancement
Symbol table munging => Inversion-Of-Control and Aspect-Oriented-Programming
frameworks
automatic typecasting and Typeglobs (DWIM assignments) => JDK1.5 "autoboxing"

The big thing that Perl has, that the others don't is that they can be written
in a "functional" way (i.e. function calls, like C) or in an OO way (i.e. like
Java or Ruby), and even using imperative programming (i.e. like Klingon).

I think it's no surprise that Larry Wall, the creator of Perl, is a linguist,
which explains a lot of Perl's flexibility - particularly with regard to syntax.
It's easy to write mini-languages (i.e. "protocol implementations") in Perl.
Does your language speak "SMTP"? There's a ton of stuff on CPAN, arguably the
real "pearl" in the Perl world.

Mike/

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