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README
batch.sh
clj-compile.sh
clj-run.sh
fasta.clj-1.clj
fasta.clj-10.clj
fasta.clj-11.clj
fasta.clj-2.clj
fasta.clj-3.clj
fasta.clj-4.clj
fasta.clj-5.clj
fasta.clj-6.clj
fasta.clj-7.clj
fasta.clj-8.clj
fasta.clj-9.clj
fasta.ghc-2.ghc
fasta.java-2.java
fasta.java-3.java
fasta.java-4.java
fasta.jruby
fasta.jruby-4.jruby
fasta.jruby-5.jruby
fasta.perl-4.perl
fasta.sbcl
fasta.sbcl_compile
fasta.sbcl_run
ghc-compile.sh
ghc-run.sh
java-compile.sh
java-run.sh
readme.txt
sbcl-compile.sh
sbcl-run.sh

README

I performance tests on my system, I got a faster program using linear
search (e.g. clj-6, clj-7) versus binary search (clj-1 through clj-5)
for looking up the gene characters in the cumulative distribution
function.  With the binary search a macro was a little faster than a
function call, but linear search right inside of fill-random! beat
them both.

I also got a little faster results using byte-based output (clj-6)
rather than char/String-based output (clj-1 through clj-5, and clj-7).


On Feb 20 2013, the fastest Clojure program for the 4-core 64-bit
machine was fasta.clojure-5.clojure, which is identical to my
fasta.clj-8.clj except for the URL in the second comment line.

The fastest Java program was fasta.java-4.java


The fastest Clojure program for the fasta-redux problem was
fasta.clojure-4.clojure, which is very similar to my fasta.clj-11.clj,
but there are many small differences.  I didn't notice any changes
that should account for changes in speed, but it wasn't obvious.

The fastest Java program for the fasta-redux problem was
fastaredux.java-3.java, which is identical to the file I copied and
called fasta.java-3.java except for the class name and comment line
with URL.