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  • Faster way to split a string and count characters using R?

    - by chrisamiller
    I'm looking for a faster way to calculate GC content for DNA strings read in from a FASTA file. This boils down to taking a string and counting the number of times that the letter 'G' or 'C' appears. I also want to specify the range of characters to consider. I have a working function that is fairly slow, and it's causing a bottleneck in my code. It looks like this: ## ## count the number of GCs in the characters between start and stop ## gcCount <- function(line, st, sp){ chars = strsplit(as.character(line),"")[[1]] numGC = 0 for(j in st:sp){ ##nested ifs faster than an OR (|) construction if(chars[[j]] == "g"){ numGC <- numGC + 1 }else if(chars[[j]] == "G"){ numGC <- numGC + 1 }else if(chars[[j]] == "c"){ numGC <- numGC + 1 }else if(chars[[j]] == "C"){ numGC <- numGC + 1 } } return(numGC) } Running Rprof gives me the following output: > a = "GCCCAAAATTTTCCGGatttaagcagacataaattcgagg" > Rprof(filename="Rprof.out") > for(i in 1:500000){gcCount(a,1,40)}; > Rprof(NULL) > summaryRprof(filename="Rprof.out") self.time self.pct total.time total.pct "gcCount" 77.36 76.8 100.74 100.0 "==" 18.30 18.2 18.30 18.2 "strsplit" 3.58 3.6 3.64 3.6 "+" 1.14 1.1 1.14 1.1 ":" 0.30 0.3 0.30 0.3 "as.logical" 0.04 0.0 0.04 0.0 "as.character" 0.02 0.0 0.02 0.0 $by.total total.time total.pct self.time self.pct "gcCount" 100.74 100.0 77.36 76.8 "==" 18.30 18.2 18.30 18.2 "strsplit" 3.64 3.6 3.58 3.6 "+" 1.14 1.1 1.14 1.1 ":" 0.30 0.3 0.30 0.3 "as.logical" 0.04 0.0 0.04 0.0 "as.character" 0.02 0.0 0.02 0.0 $sampling.time [1] 100.74 Any advice for making this code faster?

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  • Remove first and last characters from a string in Lisp

    - by powerj1984
    I am passing in command line arguments to my Lisp program and they are formatted like this when they hit my main function: ("1 1 1" "dot" "2 2 2") I have a dot function and would like to call it directly from the argument, but first I must strip the " characters. I tried variations of this function: (defun remove-quotes (s) (setf (aref s 0) '"")) to no avail, Lisp complains that "" is not a member of base-char. Thanks!

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  • Deserialize Stream to List<T> or any other type

    - by Sam
    Attempting to deserialize a stream to List<T> (or any other type) and am failing with the error: The type arguments for method 'Foo.Deserialize<T>(System.IO.Stream)' cannot be inferred from the usage. Try specifying the type arguments explicitly. This fails: public static T Deserialize<T>(this Stream stream) { BinaryFormatter bin = new BinaryFormatter(); return (T)bin.Deserialize(stream); } But this works: public static List<MyClass.MyStruct> Deserialize(this Stream stream) { BinaryFormatter bin = new BinaryFormatter(); return (List<MyClass.MyStruct>)bin.Deserialize(stream); } or: public static object Deserialize(this Stream stream) { BinaryFormatter bin = new BinaryFormatter(); return bin.Deserialize(stream); } Is it possible to do this without casting, e.g. (List<MyStruct>)stream.Deserialize()?

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  • jQuery + Validation plugin: add/remove class to/from element's parent

    - by FreekOne
    Hi guys, I'm working with the jQuery Validation plugin and I wrote the following code which adds a class to the element's parent if not valid (as well as inserting the actual error message at a particular location within the parent): errorPlacement: function(error, element) { element.parent().addClass('error'); error.insertBefore(element.parent().children("br")); } This works, however, if a field's content is corrected and becomes valid, the class obviously doesn't get removed from its parent (actually, neither does the error element, instead it just gets a display: none; CSS property). How can I check if an element becomes valid and remove its parent class if so ? Any help would be much appreciated, thank you !

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  • Efficient way in Python to add an element to a comma-separated string

    - by ensnare
    I'm looking for the most efficient way to add an element to a comma-separated string while maintaining alphabetical order for the words: For example: string = 'Apples, Bananas, Grapes, Oranges' addition = 'Cherries' result = 'Apples, Bananas, Cherries, Grapes, Oranges' Also, a way to do this but while maintaining IDs: string = '1:Apples, 4:Bananas, 6:Grapes, 23:Oranges' addition = '62:Cherries' result = '1:Apples, 4:Bananas, 62:Cherries, 6:Grapes, 23:Oranges' Sample code is greatly appreciated. Thank you so much.

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  • Insert character infront of each word in a string using C++

    - by insertable
    Hi all, I have a string, for example; "llama,goat,cow" and I just need to put a '@' in front of each word so my string will look like "@llama,@goat,@cow", but I need the values to be dynamic also, and always with a '@' at the beginning. Not knowing a great deal of C++ could someone please help me find the easiest solution to this problem? Many thanks in advance.

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  • PHP image resize using nearest-neighbor interpolation?

    - by shipshape
    I have a 16x16 sprite in PNG or GIF image format, and would like to display it on a website at 64 x 64 in all its pixelated glory. In Firefox 3.6+ and IE I can do this easily with CSS using image-rendering and -ms-interpolation-mode, but as this doesn't work in all browsers I'd like to resize the image on the fly using PHP instead. What's the best way to resize images using nearest-neighbor interpolation in PHP?

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  • How to scale an image (in data URI format) in JavaScript (real scaling, not using styling)

    - by 103067513055141045393
    We are capturing a visible tab in a Chrome browser (by using the extensions API chrome.tabs.captureVisibleTab) and receiving a snapshot in the data URI scheme (Base64 encoded string). Is there a JavaScript library that can be used to scale down an image to a certain size? Currently we are styling it via CSS, but have to pay performance penalties as pictures are mostly 100 times bigger than required. Additional concern is also the load on the localStorage we use to save our snapshots. Does anyone know of a way to process this data URI scheme formatted pictures and reduce their size by scaling them down? References: Data URI scheme on http://en.wikipedia.org/wiki/Data_URI_scheme Chrome Extensions API onhttp://code.google.com/chrome/extensions/tabs.html The "Recently Closed Tabs" Chrome Extension onhttp://code.google.com/p/recently-closed-tabs

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  • How to sort a key of a map

    - by Tsuna Sawada
    How to sort (any kind of sorting) a key of a map(treemap or hashmap) i have a problem and it goes like this. i have a map that has a key of 27527-683, 27525-1179, 27525-1571, 27525-1813, 27525-4911, 27526-1303, 27526-3641, 27525-3989, 27525-4083, 27525-4670, 27526-4102, 27526-558, 27527-2411, 27527-4342 this is the list of keys and the value for each of the key is a list. now, how can i sort this key in ascending order by number. ex. if i want to sort : 1,2,11,20,31,3,10 i want to have as output is : 1,2,3,10,11,20,31 but when i use the autosort of treemap the output goes : 1,10,11,2,20,3,31 how can i sort it in ascending order by numeric? please help me. i can't think of anymore ways because this is my first time handling map and list

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  • PHP - Resize an image and fill gaps of proportions with a color

    - by Kerry
    I am uploading logos to my system, and they need to fix in a 60x60 pixel box. I have all the code to resize it proportionately, and that's not a problem. My 454x292px image becomes 60x38. The thing is, I need the picture to be 60x60, meaning I want to pad the top and bottom with white each (I can fill the rectangle with the color). The theory is I create a white rectangle, 60x60, then I copy the image and resize it to 60x38 and put it in my white rectangle, starting 11px from the top (which adds up to the 22px of total padding that I need. I would post my code but it's decently long, though I can if requested. Does anyone know how to do this or can you point me to code/tutorial that does this?

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  • Python proper use of __str__ and __repr__

    - by Peter
    Hey, My current project requires extensive use of bit fields. I found a simple, functional recipe for bit a field class but it was lacking a few features I needed, so I decided to extend it. I've just got to implementing __str__ and __repr__ and I want to make sure I'm following convention. __str__ is supposed to be informal and concice, so I've made it return the bit field's decimal value (i.e. str(bit field 11) would be "3". __repr__ is supposed to be a official representation of the object, so I've made it return the actual bit string (i.e. repr(bit field 11) would be "11"). In your opinion would this implementation meet the conventions for str and repr? Additionally, I have used the bin() function to get the bit string of the value stored in the class. This isn't compatible with Python < 2.6, is there an alternative method? Cheers, Pete

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  • How to remove the file extension in a zsh completion?

    - by meeselet
    I want to adjust zsh so that I can tab complete: myprog <tab> using all *.foo files in ~/somedir, but have it so that it displays them without the .foo extension. Is there any way to do this? This is what I have so far: #compdef myprog typeset -A opt_args local context state line local -a mydirs mydirs="(. ~/somedir)" _arguments -s -S \ "*:name:->foos" \ && return 0 case $state in (foos) _files -W ${mydirs} -g '*.foo(:r)' && return 0 ;; esac return 1 However, this displays double the output for every file (that is, each .foo file is listed with and without its extension). Is there any way around this?

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  • c# string.replace in foreach loop

    - by paradox
    Somehow I can't seem to get string replacement within a foreach loop in C# to work. My code is as follows : foreach (string s in names) { s.Replace("pdf", "txt"); } Am still quite new to LINQ so pardon me if this sounds amateurish ;)

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  • use jQuery to get 'true size' of image without removing the class

    - by jon3laze
    I am using Jcrop on an image that is resized with css for uniformity. JS <script type="text/javascript"> $(window).load(function() { //invoke Jcrop API and set options var api = $.Jcrop('#image', { onSelect: storeCoords, trueSize: [w, h] }); api.disable(); //disable until ready to use //enable the Jcrop on crop button click $('#crop').click(function() { api.enable(); }); }); function storeCoords(c) { $('#X').val(c.x); $('#Y').val(c.y); $('#W').val(c.w); $('#H').val(c.h); }; </script> HTML <body> <img src="/path/to/image.jpg" id="image" class="img_class" alt="" /> <br /> <span id="crop" class="button">Crop Photo</span> <span id="#X" class="hidden"></span> <span id="#Y" class="hidden"></span> <span id="#W" class="hidden"></span> <span id="#H" class="hidden"></span> </body> CSS body { font-size: 13px; width: 500px; height: 500px; } .image { width: 200px; height: 300px; } .hidden { display: none; } I need to set the h and w variables to the size of the actual image. I tried using the .clone() manipulator to make a copy of the image and then remove the class from the clone to get the sizing but it sets the variables to zeros. var pic = $('#image').clone(); pic.removeClass('image'); var h = pic.height(); var w = pic.width(); It works if I append the image to an element in the page, but these are larger images and I would prefer not to be loading them as hidden images if there is a better way to do this. Also removing the class, setting the variables, and then re-adding the class was producing sporadic results. I was hoping for something along the lines of: $('#image').removeClass('image', function() { h = $(this).height(); w = $(this).width(); }).addClass('image'); But the removeClass function doesn't work like that :P

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  • Pass first element of jsp list to javascript

    - by Lucian Enache
    Ok so I'm trying to access the first element of a JSP list, here's what I've come up with so far without any kind of luck: onclick="alert('<%=list[0]%>');" What's the best approach to access the first element and eventually to pass it to a javascript variable/function ? I've heard that the <% %> tags are deprecated and some are suggesting relaying on JSTL/EL how can one use those without having to iterate the entire list and put a breakpoint for the iterators ?

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  • C Check Substring of a String C

    - by user69514
    I'm trying to check whether or not the second argument in my program is a substring of the first argument. The problem is that it only work if the substring starts with the same letter of the string. EDIT: It must be done in C, not C++. Sorry #include <stdio.h> #include <string.h> int my_strstr( char const *s, char const *sub ) { char const *ret = sub; while ( ret = strchr( ret, *sub ) ) { if ( strcmp( ++ret, sub+1 ) == 0 ) return 1; } return 0; } int main(int argc, char **argv){ if (argc != 3) { printf ("Usage: check <string one> <string two>\n"); } int result = my_strstr(argv[1], argv[2]); if(result == 1){ printf("%s is a substring of %s\n", argv[2], argv[1]); } else{ printf("%s is not a substring of %s\n", argv[2], argv[1]); } return 0; }

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  • Delete all characters in a multline string upto a given pattern

    - by biffabacon
    Using Python I need to delete all charaters in a multiline string up to the first occurrence of a given pattern. In Perl this can be done using regular expressions with something like: #remove all chars up to first occurrence of cat or dog or rat $pattern = 'cat|dog|rat' $pagetext =~ s/(.*)($pattern)/$2/xms; What's the best way to do it in Python?

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