DNA: C, G, A, T, \n
On Sat, Mar 17, 2012 at 02:23:48AM +0900, Francois????Charles Matthieu????Berenger wrote: > ｈｉ philippe, > > i am curious, is your string a dna sequencｅｓｏ ｔｈａｔ ｓ ｗｈｙ ｉｔ ｉｓ ｓｏ ｌｏｎｇ？ > > ｒｅｇａｒｄｓ，ｆ > > > On Fri, 16 Mar 2012 10:14:41 -0400 > Edgar Friendly <thelema...@gmail.com> wrote: > > > On 03/16/2012 09:03 AM, Philippe Veber wrote: > > > Dear camlers, > > > > > > Say that you'd like to search a regexp on a file with lines so long that > > > you'd rather not load them entirely at once. If you can bound the size > > > of a match by k << length of a line, then you know that you can only > > > keep a small portion of the line in memory to search the regexp. > > > Typically you'd like to access substrings of size k from left to right. > > > I guess such a thing should involve buffered inputs and avoid copying > > > strings as much as possible. My question is as follows: has anybody > > > written a library to access these substrings gracefully and with decent > > > performance? > > > Cheers, > > > Philippe. > > > > > This is tricky to do, as incremental matching implies DFA-based > > matching, but returning matching substrings implies backtrack-based > > matching. The re2 library returns matching substrings by matching > > forward to find the end of patterns, and then matching backwards on the > > reversed regex from that point to find their beginning. I don't know if > > even it supports this on incremental input. > > > > Subject to the assumption that starting to match implies either > > finishing or aborting a match (i.e. once you've started to match your > > regex, no other match will start before either this match attempt > > finishes successful or not), this is not unreasonable to do. Without > > this assumption, it requires tracking many match start locations and > > somehow knowing which of them match or fail to match. I'm not sure this > > has been done before. > > > > E. > > > > -- > > Caml-list mailing list. Subscription management and archives: > > https://sympa-roc.inria.fr/wws/info/caml-list > > Beginner's list: http://groups.yahoo.com/group/ocaml_beginners > > Bug reports: http://caml.inria.fr/bin/caml-bugs > > > > > > > -- > Caml-list mailing list. Subscription management and archives: > https://sympa-roc.inria.fr/wws/info/caml-list > Beginner's list: http://groups.yahoo.com/group/ocaml_beginners > Bug reports: http://caml.inria.fr/bin/caml-bugs > -- Caml-list mailing list. Subscription management and archives: https://sympa-roc.inria.fr/wws/info/caml-list Beginner's list: http://groups.yahoo.com/group/ocaml_beginners Bug reports: http://caml.inria.fr/bin/caml-bugs
