August 2006 - Boost-users - lists.preview.boost.org

little endian detection
by Andreas Fabri 29 Aug '06

29 Aug '06

Hello, Is boost supported for Visual C++ 8 in 64 bit mode on XP 64 on an AMD Turion. When I run cl.exe /E boost/detail/endian.hpp I get the error message that it must be set up correctly. I use boost-1_33_1 coming with cygwin. thanks in advance, andreas

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Re: [Boost-users] Mismatch and regex newbie problem still problem
by james.jones＠firstinvestors.com 29 Aug '06

29 Aug '06

From: "david v" <danova_fr(a)hotmail.com> > Yes i think there were some misunderstanding here.. I think that comes by > the definition you have of mistake. A mistake for me is as follows: > > Regex: "testing" > String_to_search: "tastung". > The output should be that the regex testing was found but with 2 mismatches > that are "a" and "u". So a mismatch is a letter that was not found. > > It may sound weird to you but the way i'm using the regex is to identify > genomic regions, so in other words for biological applications. > In some cases my regex is a piece of DNA such as "atgcta" and i want to > search for this regex in another piece of DNA. Given the fact that the regex > "atgcta" can be found in the genome many times i will get probably get a lot > of matches. But in some cases i want to be able to search for "atgcta" but i > want to allow some mismatches. Obviuously i will even get more matches but i > think regex can be a more much efficient way that by building ip aligment > matrices. > > Any idea how to handle the example above I don't see how regex can help you here. You need to use more complicated string algorithms. Try this: http://en.wikipedia.org/wiki/Suffix_tree - James

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Re: [Boost-users] Mismatch and regex newbie problem still problem
by Nat Goodspeed 29 Aug '06

29 Aug '06

> -----Original Message----- > From: boost-users-bounces(a)lists.boost.org [mailto:boost-users- > bounces(a)lists.boost.org] On Behalf Of david v > Sent: Tuesday, August 29, 2006 9:08 AM > To: boost-users(a)lists.boost.org > Subject: [Boost-users] Mismatch and regex newbie problem still problem > > So to sum-up. > If the regex i'm looking for is "testing" and the string to search the > regex > for is "tastung" (obviously this is a short example but i'm dealing with > more complex regular expressions. > > how can i get the number of mismatches. Basically the output of the > program > would tell me: > >2 mismatches found in string "tastung" at position 2 (a) and 5(u). [Nat] Maybe I'm completely misunderstanding you. If so, please forgive me. I think you're saying that you want to start with the regex "testing" and have the library detect that the string "tastung" is somehow similar but nonetheless distinct. My belief is that, given the regex "testing", the library will not recognize the string "tastung" in any way. It will simply report that no match was found. You could construct a more complex regex that would handle this particular example. You could, for instance, say that you want to match a "t", followed by an arbitrary character, followed by "st", followed by another arbitrary character, followed by "ng". The library would report that the string "tastung" matches that regex, and you could ask it to tell you the specific substrings matching the variable parts. But if you want to allow arbitrary variance in any character position -- as long as some other set of character positions matches -- then I'm a little perplexed as to how to express that in a regular expression. Maybe an exhaustive family of acceptable alternatives? But if you're dealing with longer expression strings, that could explode really quickly. I think you need to get really specific about the rules you want to use to detect a "mismatch." Then you need to figure out whether the regex library is the right tool to help you apply those rules. Again, sorry if I'm way off base here.

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Efficiacy of std::vector
by Janos Vegh 29 Aug '06

29 Aug '06

Hi, I was interested in the efficiacy of std::vector. Using the test program below, I receive the following results. The "simple" handling is equivalent with the C array access. The [] and iterator access time of the vector element is an order of magnitude worse, than that of the simple access. This is not because of index limit control, it is done by at() and its use increases that access time by a factor of three. What is going on in the background here, that the implementation is so ineffective? ( I did my tests with WinXP/cygwin/g++/time, using different setting of the #define-s at the beginning) Shall I expect similar ineffectivity with the other STL objects? Regards Janos Empty cycle real 0m2.173s user 0m1.892s sys 0m0.080s STL=1, SIMPLE=1, size=0 real 0m4.917s user 0m4.646s sys 0m0.070s STL=1, size=0 real 0m33.939s user 0m33.658s sys 0m0.090s STL=1, ITERATOR=1, size=1000 real 0m34.059s user 0m33.688s sys 0m0.100s STL=1, AT=1, size=1000 real 1m22.769s user 1m22.368s sys 0m0.090s #define STL 1 #define SIMPLE 0 #define ITERATOR 1 #define AT 0 #define EMPTY 1 #if STL #include <vector> #endif using namespace std; #include <iostream> #define ARR_SIZE 1000 #define CYCLES 1000000 main (int argc, char** argv) { long int i,j,*P; #if EMPTY cout << "Empty cycle"; #else #if STL #if ITERATOR || AT std::vector<long int>::iterator pos; std::vector<long int> arr(ARR_SIZE); #else std::vector <long int> arr; arr.reserve(ARR_SIZE); #endif cout << "STL=1"; #if SIMPLE cout << ", SIMPLE=1"; #endif #if ITERATOR cout << ", ITERATOR=1"; #endif #if AT cout << ", AT=1"; #endif cout << ", size=" << arr.size(); #else long int *arr; arr = new long int[ARR_SIZE]; cout << "STL=0"; #endif #endif cout << endl; #if SIMPLE && STL P = &arr[0]; #endif for(j=0;j<CYCLES; j++) { #if STL && ITERATOR && !EMPTY i = 0; for(pos=arr.begin(); pos < arr.end(); ++pos) { *pos = i; } #else for(i=0; i<ARR_SIZE; i++) { #if !EMPTY #if SIMPLE && STL P[i] = i; #elif STL && AT arr.at(i) = i; #else arr[i] = i; #endif #endif } #endif } exit(0); }

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Re: [Boost-users] Mismatch and regex newbie problem
by david v 29 Aug '06

29 Aug '06

What's boost_check and what's it got to do with regex? john i found the boost_check in here http://www.boost.org/libs/test/doc/components/test_tools/reference/BOOST_CH… and though it would do what i was trying to do. But i think the the regex_token_iterator you submitted would do it. std::string::const_iterator start = in.begin(); std::string::const_iterator end = in.end(); boost::sregex_token_iterator i(start, end, *regex, -1), j; while(i != j) { cout << *i << endl; }

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Re: [Boost-users] Mismatch and regex newbie problem
by david v 29 Aug '06

29 Aug '06

For example, If the regex to search for is "test" and the string is "tast" , then 1 mismatch is found position 2. John, i think the code below you have submitted is doing exactly what i want right ?? std::string::const_iterator start = in.begin(); std::string::const_iterator end = in.end(); boost::sregex_token_iterator i(start, end, *regex, -1), j; while(i != j) { cout << *i << endl; } >Hello, >I'm using the boost regex library to search short expressions in large >strings. The code below works fine but it almost does what ever i >want. The thing i'm missing and that i'm not sure to handle are the >mismatches. Basically when i look for a regex in a string i want to >have the possibility to get the number of mismatches and their >respective positions. I read through the docs and saw that the >boost_check may do the work. Well the think is that i'm not sure how >to use it with my code and since the boost library is quite complex >it would be great if somebody could help to move forward. > >How can i use the code below to get the mismatches and their >positions with boost_check ??? What's boost_check and what's it got to do with regex? >#####Setting the regex >..... >re = "test"; >boost::regex *regex = new boost::regex(re,boost::regbase::icase); >..... > >#######Getting the matched >....... >std::string::const_iterator start = in.begin(); >std::string::const_iterator end = in.end(); >boost::smatch match; >while >(boost::regex_search(start,end,match,*regex,boost::match_extra)) >{ >cout << match.[0] << endl; >start = match[0].second; >} > >#############Getting the mismatches ??? >How ??? > >Any help would be extemely helpful !!! What do you mean by mismatches? The sections of the string that didn't match? That would be: std::string::const_iterator start = in.begin(); std::string::const_iterator end = in.end(); boost::smatch match; while(boost::regex_search(start,end,match,*regex)) { cout << match.prefix() << endl; start = match[0].second; } // avoid a fencepost error: cout << match.suffix() << endl; Note that the match_extra flag is unnecessary unless you really need to record repeated captures. Normal capture information - of the kind you get from Perl and other regex engines don't need this - and it slows down matching as well as requiring building the lib in a non-default mode. You can also do this rather easier with regex_token_iterator: std::string::const_iterator start = in.begin(); std::string::const_iterator end = in.end(); boost::sregex_token_iterator i(start, end, *regex, -1), j; while(i != j) { cout << *i << endl; } HTH, John.

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Mismatch and regex newbie problem
by david v 29 Aug '06

29 Aug '06

Hello, I'm using the boost regex library to search short expressions in large strings. The code below works fine but it almost does what ever i want. The thing i'm missing and that i'm not sure to handle are the mismatches. Basically when i look for a regex in a string i want to have the possibility to get the number of mismatches and their respective positions. I read through the docs and saw that the boost_check may do the work. Well the think is that i'm not sure how to use it with my code and since the boost library is quite complex it would be great if somebody could help to move forward. How can i use the code below to get the mismatches and their positions with boost_check ??? #####Setting the regex ..... re = "test"; boost::regex *regex = new boost::regex(re,boost::regbase::icase); ..... #######Getting the matched ....... std::string::const_iterator start = in.begin(); std::string::const_iterator end = in.end(); boost::smatch match; while (boost::regex_search(start,end,match,*regex,boost::match_extra)) { cout << match.[0] << endl; start = match[0].second; } #############Getting the mismatches ??? How ??? Any help would be extemely helpful !!! david

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[program_options] passing a negative numer as an option --sorry
by imre＠u-tx.com 29 Aug '06

29 Aug '06

Sorry, it was a configuration problem on my side.

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[preprocessor] Enumerating sequence and shifter sequence
by Roman Perepelitsa 29 Aug '06

29 Aug '06

Hi. I have the following sequence #define SEQ (a)(b)(c)(d) I want to transform it to something like this F(a,b) F(b,c) F(c,d) How can I do it efficiently and elegantly? Thank you in advance. Roman Perepelitsa.

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[program_options] passing a negative numer as an option
by imre＠u-tx.com 29 Aug '06

29 Aug '06

Hi, Is subj. possible (with 1.33)? If yes, then how? If I write attn = "-11" into the config file, then cout << vm["attn"].as<int16_t>(); outputs 11. Thx ImRe

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