Hi all.

Ported my research project to clojure, and now just benchmarking parts
of it. I am currently spending about 5/6th of all simulation time
doing regular expressions, so I looked into alternative regex engines,
optimizing the regular expression and trying to find out whether
clojure's (re-pattern also compiles the regex.

This old website lists the performance of several regex engines (the
fastest ones are also 'incomplete' compared to the other ones):
http://www.tusker.org/regex/regex_benchmark.html , and I am trying to
get one of them to run in clojure. As I've no experience with java, I
am struggling a bit.

(add-classpath "file:///home/boris/projects/chapter4/automaton.jar")
(import '(brics.automaton.RegExp))
(import '(brics.automaton.Automaton))
(import '(brics.automaton.RunAutomaton))

The above all loads fine, but the examples on the brics website
(http://www.brics.dk/~amoeller/automaton/faq.html ), is quite
minimal.. and I tried a few guesses how to call it through clojure [I
tried (.. new Regex ("ana")), for example]. Any help with translating
the syntax in this example to the clojure version would be
appreciated!

[java example:]
RegExp r = new RegExp("ab(c|d)*");
Automaton a = r.toAutomaton();
String s = "abcccdc";
System.out.println("Match: " + a.run(s)); // prints: true


[example of a typical string and regex in the model]
"GEDFFEDBGBFEBADACACAFGCBGDDEGGEFDFFFGDCGFGAEAGCFFBCDDCDEBCDAAFDCECCGABCGAAABBBCAFGACAABGFEBDACDFEAAGFGCGDFDGDAAEBFBGBCBDAFDFGFBCFBEABECBBAAEBABGAGFBBAAFFGGBDABFGFAFAEBBBACGEACCEBBCAFDGCADEBGCGFEEEFEADBCGCFBCEFGGGECEGEDCFCCBADBEABCCFGEADDDBEDBBFDBFDCBGDAEFECDEBFGBCBCCBEDEFGGEGCEABAFGECGCACFEGDDAEBAACDBFCGCEAEFEBBABAACFEECFDEAFFGAFEFBDCFCABEEBACBFDCEEAFFBCEDAFFDACEAABBEGFCGDCBFFBBFDDDEEBFCEGCFEFCAAGGEBBGDBCEEGFCFDDFBBFECEGGDBEFBGABFBGEACGAADAFBBDEAGDBADEECAEAAGEGEFEDCABBGFGBEFEFACEBEFFGFCFFFFFFDCB"

((?=([ BD][ ABCDF][ FG][ ABDEF][ ABCDFG][ ABCDEFG][ BCEG][ ABEG]
[ BCDEFG]))


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