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  • Java looping through array - Optimization

    - by oudouz
    I've got some Java code that runs quite the expected way, but it's taking some amount of time -some seconds- even if the job is just looping through an array. The input file is a Fasta file as shown in the image below. The file I'm using is 2.9Mo, and there are some other Fasta file that can take up to 20Mo. And in the code im trying to loop through it by bunches of threes, e.g: AGC TTT TCA ... etc The code has no functional sens for now but what I want is to append each Amino Acid to it's equivalent bunch of Bases. Example : AGC - Ser / CUG Leu / ... etc So what's wrong with the code ? and Is there any way to do it better ? Any optimization ? Looping through the whole String is taking some time, maybe just seconds, but need to find a better way to do it. import java.io.BufferedReader; import java.io.File; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; public class fasta { public static void main(String[] args) throws IOException { File fastaFile; FileReader fastaReader; BufferedReader fastaBuffer = null; StringBuilder fastaString = new StringBuilder(); try { fastaFile = new File("res/NC_017108.fna"); fastaReader = new FileReader(fastaFile); fastaBuffer = new BufferedReader(fastaReader); String fastaDescription = fastaBuffer.readLine(); String line = fastaBuffer.readLine(); while (line != null) { fastaString.append(line); line = fastaBuffer.readLine(); } System.out.println(fastaDescription); System.out.println(); String currentFastaAcid; for (int i = 0; i < fastaString.length(); i+=3) { currentFastaAcid = fastaString.toString().substring(i, i + 3); System.out.println(currentFastaAcid); } } catch (NullPointerException e) { System.out.println(e.getMessage()); } catch (FileNotFoundException e) { System.out.println(e.getMessage()); } catch (IOException e) { System.out.println(e.getMessage()); } finally { fastaBuffer.close(); } } }

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  • Can I use a attribute to make .net impersonate another user?

    - by Rising Star
    I am familiar with impersonating an account in .net by using: dim myIdentity as WindowsIdentity = someIdentity using ctx as WindowsImpersonationContext = myIdentity.Impersonate() doStuff() end using Is it possible to define a .net attribute so that I could write something like: < runAsUser(someIdentity) public sub doStuff() and then have the .net framework always impersonate when running the method doStuff()?

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  • Wont Let Me Type In My Pass Phrase

    - by Tapha
    Not real information: $ ssh-keygen -t rsa -C "[email protected]" Generating public/private rsa key pair. Enter file in which to save the key (/c/Users/Tekkub/.ssh/id_rsa): ssh.txt I entered a file name here. Not sure if i should have, Enter passphrase (empty for no passphrase): I am stuck here. I type and it doesnt work

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  • Static page routing in Sinatra (Ruby)

    - by JP
    You can serve static files with Sinatra by placing them in public/ (by default) -- I have an index.html in there at the moment, but how can I make the root point to that file without having to parse it as a template? To be clear, I can access /index.html successfully, and I'd like to route / to be the same static file, but without redirecting. Any idea how to do this?

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  • How to return a value based on the type of the generic T

    - by Blankman
    I have a method like: public T Get<T>(string key) { } Now say I want to return "hello" if the type is a string, and 110011 if it is type int. how can I do that? typeof(T) doesn't seem to work. I ideally want to do a switch statement, and return something based on the Type of the generic (string/int/long/etc). Is this possible?

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  • Creating instance of interface in C#

    - by Max
    I'm working with MS Excel interop in C# and I don't understand how this particular line of code works: var excel = new Microsoft.Office.Interop.Excel.Application(); where Microsoft.Office.Interop.Excel.Application is an INTERFACE defined as: [Guid("000208D5-0000-0000-C000-000000000046")] [CoClass(typeof(ApplicationClass))] public interface Application : _Application, AppEvents_Event { } I'm thinking that some magic happens when the interface is decorated with a CoClass attribute, but still how is it possible that we can create an instance of an interface with a new keyword? Shouldn't it generate a compile time error?

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  • serve static play2.x content from CDN

    - by Adam Lane
    In development mode I would like to have assets served locally and when deployed in production I would like them served from the CDN. Anyone using play2 and serving content from CDN be willing to share how they are doing it? // Thinking of something like this in the routes file... @if(play.Play.isDev()) { GET /assets/*file controllers.Assets.at(path="/public", file) } else { GET CDNPATH/assets/*file controllers.Assets.at(path="CDNPATH", file) } (Note: using 2.0.2 because of the headers fix https://github.com/playframework/Play20/pull/276)

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  • Repository Pattern : Add Item

    - by No Body
    Just need to clarify this one, If I have the below interface public interface IRepository<T> { T Add(T entity); } when implementing it, does checking for duplication if entity is already existing before persist it is still a job of the Repository, or it should handle some where else?

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  • How can I call a method given only its name?

    - by mfolnovich
    I'm trying to have method void run( string method ) which would run method in that class. For example: class Foo { public: void run( string method ) { // this method calls method *method* from this class } void bar() { printf( "Function bar\n" ); } void foo2() { printf( "Function foo2\n" ); } } Foo foo; int main( void ) { foo.run( "bar" ); foo.run( "foo2" ); } this would print: Function bar Function foo2 Thanks! :)

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  • saving an image object in sql server database from action method

    - by user3532152
    [HttpPost] public void Test(HttpPostedFileBase file) { UsersContext db = new UsersContext(); byte[] image = new byte[file.ContentLength]; file.InputStream.Read(image, 0, image.Length); CrimeReport i = new CrimeReport { ImageId=1, ImageName="Anjli",ImageContent = image, Active=true }; db.CrimeReports.Add(i); db.SaveChanges(); } I am getting an exception on db.CrimeReports.Add(i);

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  • Passing C string reference to C#

    - by user336109
    c code extern "C" __declspec(dllexport) int export(LPCTSTR inputFile, string &msg) { msg = "haha" } c# code [DllImport("libXmlEncDll.dll")] public static extern int XmlDecrypt(StringBuilder inputFile, ref Stringbuilder newMsg) } I got an error when I try to retrieve the content of newMsg saying that I'm trying to write to a protected memory area. What is the best way to retrieve the string from c to c#. Thanks.

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  • Will the error be displayed?

    - by user281180
    I have an ajax post and in the controller I return nothing. In case there is a failure will the error message displayed with the follwoing code? [AcceptVerbs(HttpVerbs.Post)] public void Edit(Model model) { model.Save(); } $.ajax({ type: "POST", url: '<%=Url.Action("Edit","test") %>', data: JSON.stringify(data), contentType: "application/json; charset=utf-8", dataType: "html", success: function() { }, error: function(request, status, error) { alert("Error: " & request.responseText); } });

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  • (PHP) - Changing two substrings inside a string

    - by Imp4ct
    This is my BIG string BEGIN:VEVENT UID:xxxxxx DTSTAMP:xxxxxx STATUS:CONFIRMED CLASS:PUBLIC URL:xxxxxx SUMMARY:YYYYYYY DESCRIPTION:xxxxxx; YYYYYYY; DTSTART:xxxxxx DTEND:xxxxxx GEO:xxxxxx LOCATION:xxxxxx END:VEVENT I need to change position of the two "YYYYYYY" in SUMMARY/DESCRIPTION I have to replace them without being specific since it is implemented in a much larger function. (This string is already sliced out of a 3700 line - Calendar) pls help! :)

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  • Maintain state of an ASP.NET page

    - by user279521
    Hi, what is your preferred method to maintain state of an asp.net page, if it is a public website (involving shopping cart, wish-list etc). I am in the process of designing a website that will need to ensure that the user is not able to tamper with the state (such as delete cookies etc).

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  • unprotected access to member in property get

    - by Lenik
    I have a property public ObservableCollection<string> Name { get { return _nameCache; } } _nameCache is updated by multiple threads in other class methods. The updates are guarded by a lock. The question is: should I use the same lock around my return statement? Will not using a lock lead to a race condition?

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  • C# property ending with ?

    - by MicMit
    What does that mean ? public bool? Verbose { get; set; } When applied to string? , there is an error Error 11 The type 'string' must be a non-nullable value type in order to use it as parameter 'T' in the generic type or method 'System.Nullable'

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  • Accessing a numeric property in a SimpleXMLElement

    - by Webnet
    I'm trying to access the number in the below element, but I'm having trouble getting the value out of it. echo $object->0; //returns Parse error: syntax error, unexpected T_LNUMBER, expecting T_STRING or T_VARIABLE or '{' or '$' SimpleXMLElement Object ( [0:public] => 15810 ) Any ideas on how I can get that value?

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  • C++ not recognizing my class

    - by rlb.usa
    I keep getting class undefined error from Visual Studio with my C++ code. My file looks like this: namespace myProject; scope myProject{ class FreeFormWindowsWidgetWindow : public WindowsWidget{ // shell } } But when I put FreeFormWindowsWidgetWindow in the same file as my other classes, it sees it. It doesn't seem to see anything in this file. How can I fix it and keep FreeFormWidgetWindow in its own file?

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