Re^2: counting the number of 16384 pattern matches in a large DNA sequence

As of Perl 5.16.0: "study is now a no-op, presumably fixing all outstanding bugs related to study causing regex matches to behave incorrectly!"

perldelta: Other Notable Fixes

It's a shame that it's not mentioned in the POD for study directly, but really not much of a shame to see the function fade away. The few times I attempted to use it, benchmarking showed that I still hadn't found a good application for it.

Comment on Re^2: counting the number of 16384 pattern matches in a large DNA sequence

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Re^3: counting the number of 16384 pattern matches in a large DNA sequence by BrowserUk (Patriarch) on Jun 14, 2012 at 19:42 UTC
but really not much of a shame to see the function fade away Agreed. Whilst Boyer-Moore (and some of the others: Aho-Corasick; Rabin-Karp; etc.) can be beneficial for specific tasks and algorithms -- spam filters; virus detection -- they rarely live up to their promise for general purpose work. As such, the complications they add to the runtime aren't worth it for the rare occasions when they are beneficial. Especially on modern hardware with big caches and pipelines. For genomic purposes (with its often very small alphabet), it is quite trivial to setup a specialist indexing mechanism that shows far greater benefits. With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice. The start of some sanity?	[reply]

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Re^3: counting the number of 16384 pattern matches in a large DNA sequence
by BrowserUk (Patriarch) on Jun 14, 2012 at 19:42 UTC

but really not much of a shame to see the function fade away

Agreed. Whilst Boyer-Moore (and some of the others: Aho-Corasick; Rabin-Karp; etc.) can be beneficial for specific tasks and algorithms -- spam filters; virus detection -- they rarely live up to their promise for general purpose work. As such, the complications they add to the runtime aren't worth it for the rare occasions when they are beneficial. Especially on modern hardware with big caches and pipelines.

For genomic purposes (with its often very small alphabet), it is quite trivial to setup a specialist indexing mechanism that shows far greater benefits.

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

The start of some sanity?

[reply]