Re: code for 32/64 bit strtoul strtol strtoull strtoll

From	James Kuyper <jameskuyper@verizon.net>
Newsgroups	comp.lang.c
Subject	Re: code for 32/64 bit strtoul strtol strtoull strtoll
Date	2015-03-31 16:55 -0400
Organization	Self
Message-ID	<551B09BE.5080109@verizon.net> (permalink)
References	(7 earlier) <mfen05$b4f$1@speranza.aioe.org> <551aec75.2399734@news.xs4all.nl> <mfer4g$t2o$1@dont-email.me> <551AF2FC.8080802@verizon.net> <mfeu1b$ulk$1@speranza.aioe.org>

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On 03/31/2015 03:54 PM, glen herrmannsfeldt wrote:
> James Kuyper <jameskuyper@verizon.net> wrote:
> 
> (snip on base 4 and DNA)
> 
>> I would expect genetic work to treat DNA as a nucleotide string, not a
>> number. Is there any specifically numeric operation that it would be
>> reasonable to perform on nucleotide strings, one that doesn't correspond
>> to a generic string operation?
> 
> Much is done using character strings, but, as with many other problems,
> when you want to speed it up, you look for other ways of doing it.
> 
> Often enough, they are stored in integer variables, and operated on
> as one would base 4 numbers.

I can imagine storing four base codes per byte, and I can imagine
displaying them as strings with each pair of bits displayed as the
corresponding element of "ACTG".

Given that ribosomes translate base pair triplets into amino acids,
there might be some value in wasting a little space encoding only three
base pairs per byte. On the other hand, since a triplet can start with
any given base pair, depending upon where the ribosome starts reading,
that might not be worthwhile (there are particular base pair sequences
that serve to align the ribosomes to the "correct" starting point for a
given gene - there's also some cases where those alignment clues are
missing, where  multiple different proteins are encoded by the same DNA
sequence, depending upon where you start).

What I can't imagine is any meaningful use of addition, subtraction,
multiplication or division on those "numbers". Except, of course,
insofar as multiplication or division by powers of 2 would correspond to
truncation or padding of the strings representing those base pairs. But
that is NOT an example of a "numeric operation ... that doesn't
correspond to a generic string operation".

Thread

code for 32/64 bit strtoul strtol strtoull strtoll jacob navia <jacob@jacob.remcomp.fr> - 2015-03-29 17:33 +0200
  code for 32/64 bit strtoul strtol strtoull strtoll asetofsymbols@gmail.com - 2015-03-29 09:22 -0700
    Re: code for 32/64 bit strtoul strtol strtoull strtoll Barry Schwarz <schwarzb@dqel.com> - 2015-03-29 15:12 -0700
      Re: code for 32/64 bit strtoul strtol strtoull strtoll asetofsymbols@gmail.com - 2015-03-29 23:07 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Barry Schwarz <schwarzb@dqel.com> - 2015-03-29 09:44 -0700
    Re: code for 32/64 bit strtoul strtol strtoull strtoll jacob navia <jacob@jacob.remcomp.fr> - 2015-03-29 19:05 +0200
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-29 12:15 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Ben Bacarisse <ben.usenet@bsb.me.uk> - 2015-03-30 02:01 +0100
    Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-29 19:48 -0700
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Barry Schwarz <schwarzb@dqel.com> - 2015-03-29 22:08 -0700
        Re: code for 32/64 bit strtoul strtol strtoull strtoll Ben Bacarisse <ben.usenet@bsb.me.uk> - 2015-03-30 12:44 +0100
          Re: code for 32/64 bit strtoul strtol strtoull strtoll Barry Schwarz <schwarzb@dqel.com> - 2015-03-30 09:04 -0700
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Ben Bacarisse <ben.usenet@bsb.me.uk> - 2015-03-30 21:00 +0100
        Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-30 08:24 -0700
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Tim Rentsch <txr@alumni.caltech.edu> - 2015-03-30 07:21 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Ian Collins <ian-news@hotmail.com> - 2015-03-30 18:02 +1300
    Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-30 08:03 +0100
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Ian Collins <ian-news@hotmail.com> - 2015-03-30 20:33 +1300
        Re: code for 32/64 bit strtoul strtol strtoull strtoll Ian Collins <ian-news@hotmail.com> - 2015-03-30 20:35 +1300
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Tim Rentsch <txr@alumni.caltech.edu> - 2015-03-30 07:27 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-30 09:08 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-30 09:29 -0700
  Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-03-30 15:16 -0500
    Re: code for 32/64 bit strtoul strtol strtoull strtoll jacob navia <jacob@jacob.remcomp.fr> - 2015-03-31 00:15 +0200
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-03-31 01:42 -0500
    Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-30 23:39 +0100
      Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-03-31 01:44 -0500
        Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-31 13:01 +0100
          Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-03-31 05:13 -0700
          Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 08:06 -0700
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 08:26 -0700
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-31 16:40 +0100
              Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-03-31 09:39 -0700
              Re: code for 32/64 bit strtoul strtol strtoull strtoll Kaz Kylheku <kaz@kylheku.com> - 2015-03-31 18:22 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-31 19:36 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 12:11 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Kaz Kylheku <kaz@kylheku.com> - 2015-03-31 19:23 +0000
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-31 16:52 +0100
              Re: code for 32/64 bit strtoul strtol strtoull strtoll glen herrmannsfeldt <gah@ugcs.caltech.edu> - 2015-03-31 17:54 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll raltbos@xs4all.nl (Richard Bos) - 2015-03-31 18:51 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-31 20:05 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-03-31 15:18 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-03-31 20:49 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-03-31 13:06 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll raltbos@xs4all.nl (Richard Bos) - 2015-04-06 13:03 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-04-06 14:27 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-04-06 17:01 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-04-06 11:25 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-04-06 23:34 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll glen herrmannsfeldt <gah@ugcs.caltech.edu> - 2015-04-07 03:46 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-04-08 11:05 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-04-08 08:31 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll glen herrmannsfeldt <gah@ugcs.caltech.edu> - 2015-03-31 19:54 +0000
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-03-31 16:55 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-31 22:20 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 14:36 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-03-31 14:55 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-03-31 17:00 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-04-01 01:24 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll James Kuyper <jameskuyper@verizon.net> - 2015-03-31 23:33 -0400
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Richard Heathfield <rjh@cpax.org.uk> - 2015-04-01 04:42 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-03-31 20:26 +0100
            Re: code for 32/64 bit strtoul strtol strtoull strtoll Ian Collins <ian-news@hotmail.com> - 2015-04-01 10:33 +1300
              Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-04-01 04:33 -0500
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Bartc <bc@freeuk.com> - 2015-04-01 12:43 +0100
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-04-02 01:02 -0500
                Re: code for 32/64 bit strtoul strtol strtoull strtoll asetofsymbols@gmail.com - 2015-04-01 23:57 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-04-03 00:29 -0500
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Malcolm McLean <malcolm.mclean5@btinternet.com> - 2015-04-02 09:01 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Keith Thompson <kst-u@mib.org> - 2015-04-02 14:30 -0700
                Re: code for 32/64 bit strtoul strtol strtoull strtoll Robert Wessel <robertwessel2@yahoo.com> - 2015-04-03 00:39 -0500
                Re: code for 32/64 bit strtoul strtol strtoull strtoll glen herrmannsfeldt <gah@ugcs.caltech.edu> - 2015-04-01 15:55 +0000

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