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  • Parse a text file into multiple text file

    - by Vijay Kumar Singh
    I want to get multiple file by parsing a input file Through Java. The Input file contains many fasta format of thousands of protein sequence and I want to generate raw format(i.e., without any comma semicolon and without any extra symbol like "", "[", "]" etc) of each protein sequence. A fasta sequence starts form "" symbol followed by description of protein and then sequence of protein. For example ? lcl|NC_000001.10_cdsid_XP_003403591.1 [gene=LOC100652771] [protein=hypothetical protein LOC100652771] [protein_id=XP_003403591.1] [location=join(12190..12227,12595..12721,13403..13639)] MSESINFSHNLGQLLSPPRCVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAESLHHPEITFLTAFCL PSFTRSRPLPDRQLHHCLALCPSFALPAGDGVCHGPGLQGSCYKGETQESVESRVLPGPRHRH Like above formate the input file contains 1000s of protein sequence. I have to generate thousands of raw file containing only individual protein sequence without any special symbol or gaps. I have developed the code for it in Java but out put is : Cannot open a file followed by cannot find file. Please help me to solve my problem. Regards Vijay Kumar Garg Varanasi Bharat (India) The code is /*Java code to convert FASTA format to a raw format*/ import java.io.*; import java.util.*; import java.util.regex.*; import java.io.FileInputStream; // java package for using regular expression public class Arrayren { public static void main(String args[]) throws IOException { String a[]=new String[1000]; String b[][] =new String[1000][1000]; /*open the id file*/ try { File f = new File ("input.txt"); //opening the text document containing genbank ids FileInputStream fis = new FileInputStream("input.txt"); //Reading the file contents through inputstream BufferedInputStream bis = new BufferedInputStream(fis); // Writing the contents to a buffered stream DataInputStream dis = new DataInputStream(bis); //Method for reading Java Standard data types String inputline; String line; String separator = System.getProperty("line.separator"); // reads a line till next line operator is found int i=0; while ((inputline=dis.readLine()) != null) { i++; a[i]=inputline; a[i]=a[i].replaceAll(separator,""); //replaces unwanted patterns like /n with space a[i]=a[i].trim(); // trims out if any space is available a[i]=a[i]+".txt"; //takes the file name into an array try // to handle run time error /*take the sequence in to an array*/ { BufferedReader in = new BufferedReader (new FileReader(a[i])); String inline = null; int j=0; while((inline=in.readLine()) != null) { j++; b[i][j]=inline; Pattern q=Pattern.compile(">"); //Compiling the regular expression Matcher n=q.matcher(inline); //creates the matcher for the above pattern if(n.find()) { /*appending the comment line*/ b[i][j]=b[i][j].replaceAll(">gi",""); //identify the pattern and replace it with a space b[i][j]=b[i][j].replaceAll("[a-zA-Z]",""); b[i][j]=b[i][j].replaceAll("|",""); b[i][j]=b[i][j].replaceAll("\\d{1,15}",""); b[i][j]=b[i][j].replaceAll(".",""); b[i][j]=b[i][j].replaceAll("_",""); b[i][j]=b[i][j].replaceAll("\\(",""); b[i][j]=b[i][j].replaceAll("\\)",""); } /*printing the sequence in to a text file*/ b[i][j]=b[i][j].replaceAll(separator,""); b[i][j]=b[i][j].trim(); // trims out if any space is available File create = new File(inputline+"R.txt"); try { if(!create.exists()) { create.createNewFile(); // creates a new file } else { System.out.println("file already exists"); } } catch(IOException e) // to catch the exception and print the error if cannot open a file { System.err.println("cannot create a file"); } BufferedWriter outt = new BufferedWriter(new FileWriter(inputline+"R.txt", true)); outt.write(b[i][j]); // printing the contents to a text file outt.close(); // closing the text file System.out.println(b[i][j]); } } catch(Exception e) { System.out.println("cannot open a file"); } } } catch(Exception ex) // catch the exception and prints the error if cannot find file { System.out.println("cannot find file "); } } } If you provide me correct it will be much easier to understand.

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  • GetProperties() to return all properties for an interface inheritance hierarchy

    - by sduplooy
    Assuming the following hypothetical inheritance hierarchy: public interface IA { int ID { get; set; } } public interface IB : IA { string Name { get; set; } } Using reflection and making the following call: typeof(IB).GetProperties(BindingFlags.Public | BindingFlags.Instance) will only yield the properties of interface IB, which is "Name". If we were to do a similar test on the following code, public abstract class A { public int ID { get; set; } } public class B : A { public string Name { get; set; } } the call typeof(B).GetProperties(BindingFlags.Public | BindingFlags.Instance) will return an array of PropertyInfo objects for "ID" and "Name". Is there an easy way to find all the properties in the inheritance hierarchy for interfaces as in the first example?

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  • Overwriting arguments object for a Javascript function

    - by Ian Storm Taylor
    If I have the following: // Clean input. $.each(arguments, function(index, value) { arguments[index] = value.replace(/[\W\s]+/g, '').toLowerCase(); }); Would that be a bad thing to do? I have no further use for the uncleaned arguments in the function, and it would be nice not to create a useless copy of arguments just to use them, but are there any negative effects to doing this? Ideally I would have done this, but I'm guessing this runs into problems since arguments isn't really an Array: arguments = $.map(arguments, function(value) { return value.replace(/[\W\s]+/g, '').toLowerCase(); }); Thanks for any input. EDIT: I've just realized that both of these are now inside their own functions, so the arguments object has changed. Any way to do this without creating an unnecessary variable?

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  • has_many :through when join table doesn't contain FK to both tables

    - by seth.vargo
    I have a structure that isn't really a has_many :through example, but I'd like it to behave like one: # user.rb belongs_to :blog has_many :posts # post.rb belongs_to :user # blog.rb has_many :users has_many :posts, :through => :users # this obviously doesn't work becase # both FKs aren't in the blogs table I want to get ALL posts for a blog in an array. I'm aware that I can do this with Ruby using each or getting fancy with collect, but I'd like to let SQL do the work. Can someone explain how I can set up my models in a way that lets me call @blog.posts using SQL, not Ruby? Edit: I know in SQL I can write something like: SELECT * FROM posts WHERE posts.user_id IN ( SELECT users.id FROM users WHERE users.blog_id = 7 ) which obviously shows two queries are needed. I don't think this is possible with a join, but I'm not totally sure. It's obvious that a subquery is needed, but how do I get rails to build that subquery with ARel instead of having to return and use Ruby to loop and collect and such?

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  • Setting Mnemonics and Hot Keys for a JOptionPane Dialog

    - by Daniel Bingham
    Is it possible to assign hotkeys and mnemonics to the buttons in a JOptionPane Dialog? I'd like to be able, in a JOptionPane generated message dialog with the options Yes, No and Cancel, press Y to hit the Yes button, N to hit the No button and escape to activate the escape button. Similarly in a dialog with Okay and Cancel buttons I'd like to be able to activate them with enter and escape. I've attempted passing JButtons into the JOptionPane's button Object array with the Mnemonics set already. The mnemonics work and the buttons show up correctly in the dialogs, however, they do not act properly when they are activated. Most noticeably they do not dispose of the dialog. What is the correct way to add hotkeys and Mnemonics to a JOptionPane Dialog's buttons? As always, my apologies ahead of time if this is a duplicate - I searched both Google and Stackoverflow and found nothing.

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  • In Drupal, how to change the values passed to Pathauto?

    - by Vinicius Pinto
    I have Pathauto configured to generate an alias based on the title of a node, for a specific content type. The problem is that I want to make small changes in this title before Pathauto uses it to generate the alias. The first comment in this post suggests the use of hook_token_values, but I couldn't really understand how to use it, even after reading the docs. In my tests, when I implement this hook, the alias generated is always "array", which means I'm missing something. Any help? Thanks.

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  • Pear MDB2 class and raiserror exceptions in SQL Server

    - by drholzmichl
    Hi, in SQL Server it's possible to raise an error with raiserror(). I want to use a severity, which doesn't interrupt the connection. This error is raised in a stored procedure. In SQL Management Studio all is fine and I get my error code when executing this SP. But when trying to execute this SP via MDB2 in PHP5 this doesn't work. All I get is an empty array. MDB2 object is created via (including needed options): $db =& MDB2::connect($dsn); $db->setFetchMode(MDB2_FETCHMODE_ASSOC); $db->setOption('portability',MDB2_PORTABILITY_ALL ^ MDB2_PORTABILITY_EMPTY_TO_NULL); The following works (I get a PEAR error): $db->query("RAISERROR('test',11,0);"); But when calling a stored procedure which raises this error via $db->query("EXEC sp_raise_error"); there is not output. What's wrong?

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  • google search engine api not produce exact live search

    - by Bharanikumar
    Hi , The google search engine api not render the first result , Example, function google_search_api($args, $referer = 'http://localhost/test/', $endpoint = 'web'){ $url = "http://ajax.googleapis.com/ajax/services/search/".$endpoint; if ( !array_key_exists('v', $args) ) $args['v'] = '1.0'; $url .= '?'.http_build_query($args, '', '&'); $ch = curl_init(); curl_setopt($ch, CURLOPT_URL, $url); curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1); // note that the referer must be set curl_setopt($ch, CURLOPT_REFERER, $referer); $body = curl_exec($ch); curl_close($ch); //decode and return the response return json_decode($body); } $rez = google_search_api(array( 'q' = 'dl03', )); print_r($rez); the result for the above snippet little differ compare to live google search, the above snippet not render first result , that is in google live search first result not displaying the above snippet , AMy i know, what should i have to do now, Regards

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  • Statement hierarchy in programming languages

    - by sudo
    I quickly wrote an interpreter for some sort of experimental programing language i came up with, in PHP (yes, in PHP). The language itself doesn't have anything really special, I just wanted to give it a try. I got the basic things working (Hello World, input to output, string manipulation, arithmetics) but I'm getting stuck with the management of blocks and grouped statements. What I mean is: PHP and most other languages let you do this: ((2+2)*(8+2)+2), of course not only with mathematical computations. My program structure currently consists of a multidimensional array built like this: ID => Type (Identifier, String, Int, Newline, EOF, Comma, ...) Contents (If identifier, int or string) How could I allow statements to be executed in a defined order like in the PHP example above?

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  • Is NSDictionary key order guaranteed the same as initialized if it never changes?

    - by Thaurin
    I've run into the same problem as found in this question. However, I have a follow-up question. I seem to be in the same situation as the original asker: I have a plist with a hierarchy of dictionaries that define a configuration screen. These are not mutable and will stay the same throughout the application. Since the original discussion seems to focus on problems arising from mutating the dictionary, I must ask for comfirmation: is the order of a dictionary guaranteed the same as they are in the plist, i.e. as it is read (with initWithContentsOfFile)? Can I use allKeys on it in this case to get a correct-order array of keys if the dictionary never changes?

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  • Checking for Magento login on external page

    - by LinuxGnut
    I'm hitting a wall here while trying to access items from Magento on an external page (same server, same domain, etc, etc). I want to see if the user is logged into Magento before showing them certain parts on the site. Keep in mind that this code exists outside of Magento. Mage::app("default"); Mage::getSingleton("core/session", array("name" = "frontend")); if (empty($session)) { $session = Mage::getSingleton("customer/session"); } if($session-isLoggedIn()) echo "hi"; $cart = Mage::helper('checkout/cart')-getCart()-getItemsCount(); echo $cart; $cart returns 0, where I definitely have products in my cart. isLoggedIn() also returns false. What am I doing wrong here? Is there an option in Magento that I need to turn on or off to be able to access this information outside of Magento?

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  • Fibonacci sequence subroutine returning one digit too high...PERL

    - by beProactive
    #!/usr/bin/perl -w use strict; sub fib { my($num) = @_; #give $num to input array return(1) if ($num<=1); #termination condition return($num = &fib($num-1) + &fib($num-2)); #should return sum of first "n" terms in the fibonacci sequence } print &fib(7)."\n"; #should output 20 This subroutine should be outputting a summation of the first "x" amount of terms, as specified by the argument to the sub. However, it's one too high. Does this have something to do with the recursion? Thanks.

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  • what is for....in statement in javascript

    - by dramasea
    anyone can explain how to use for...in statement in javascript. I had read the w3school article but i think it is not so clear.Below is the code, please explain this: <html> <body> <script type="text/javascript"> var x; var mycars = new Array(); mycars[10] = "Saab"; mycars[20] = "Volvo"; mycars[30] = "BMW"; for (x in mycars) { document.write(mycars[x] + "<br />"); } </script> </body> </html>

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  • SQL Server 2005 Fail: Return Dates As Strings

    - by Abs
    Hello all, I am using the SQL Server PHP Driver, I think this question can be answered without knowing what this is. I have come across this many times, what does it mean by NAMES? Column names?: SET NAMES utf8 Is there a query similar to the above that will get my dates to be returned as a string? For some reason on my SQL Sever 2008 on Vista, this works: $connectionInfo = array('Database' => $dbname, 'ReturnDatesAsStrings' => true) But the above 'ReturnDatesAsStrings' does not work on my SQL Server 2005 on a windows server machine? I can't execute any queries after setting the above! Does SQL Server 2005 support ReturnDatesAsStrings? Is there some other parameter I can pass to do the same? Thanks all for any help EDIT I should of mentioned this but if there is a solution I am hoping for one that is in the form of a setting that can be set before any queries can be executed as I do not have control on what queries will be executed.

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  • CodeIgniter's Scaffolding not working

    - by 01010011
    Hi, I keep getting a 404 Page Not Found whenever I try to access CodeIgniter's Scaffolding page in my browser, like so: localhost/codeignitor/index.php/blog/scaffolding/mysecretword I can access localhost/codeignitor/index.php/blog just fine. I followed CodeIgnitor's instructions in their "Create a blog in 20 minutes" by storing my database settings in the database.php file; and automatically connecting to the database by inserting "database" in the core array of the autoload.php; and I've added both parent::Controller(); and $this-load-scaffolding('myTableName') to blog's constructor. It still gives me this 404. Any suggestions?

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  • Routing zend request through a default controller when controller not found.

    - by Brett Pontarelli
    Below is a function defined in my Bootstrap class. I must be missing something fundamental in the way Zend does routing and dispatching. What I am trying to accomplish is simple: For any request /foo/bar/* that is not dispatchable for any reason try /index/foo/bar/. The problem I'm having is when the FooController exists I get Action "foo" does not exist. Basically, the isDispatchable is always false. public function run() { $front = Zend_Controller_Front::getInstance(); $request = $front->getRequest(); $dispatcher = $front->getDispatcher(); //$controller = $dispatcher->getControllerClass($request); if (!$dispatcher->isDispatchable($request)) { $route = new Zend_Controller_Router_Route( ':action/*', array('controller' => 'index') ); $router = $front->getRouter(); $router->addRoute('FallBack', $route); } $front->dispatch(); }

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  • JSON Search and remove in php?

    - by moogeek
    Hello! I have a session variable $_SESSION["animals"] containing a deep json object with values: $_SESSION["animals"]='{ "0":{"kind":"mammal","name":"Pussy the Cat","weight":"12kg","age":"5"}, "1":{"kind":"mammal","name":"Roxy the Dog","weight":"25kg","age":"8"}, "2":{"kind":"fish","name":"Piranha the Fish","weight":"1kg","age":"1"}, "3":{"kind":"bird","name":"Einstein the Parrot","weight":"0.5kg","age":"4"}, }'; For example, I want to find the line with "Piranha the Fish" and then remove it (and json_encode it again as it was). How to do this? I guess i need to search in json_decode($_SESSION["animals"],true) resulting array and find the parent key to remove but i'm stucked anyways.

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  • Codeigniter Form validation problem

    - by ben robinson
    Please please please can someone help me $this-load-library('form_validation'); $this-load-helper('cookie'); $data = array(); if($_POST) { // Set validation rules including additional validation for uniqueness $this-form_validation-set_rules('yourname', 'Your Name', 'trim|required'); $this-form_validation-set_rules('youremail', 'Your Email', 'trim|required|valid_email'); $this-form_validation-set_rules('friendname', 'Friends Name', 'trim|required'); $this-form_validation-set_rules('friendemail', 'Friends Email', 'trim|required|valid_email'); // Run the validation and take action if($this-form_validation-run()) { echo 'valid; } } else{ echo 'problem'; } Form validation is coming back with no errors can cany one see why?

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  • Calling UITableViews delegate methods directly.

    - by RickiG
    Hi I was looking for a way to call the edit method directly. - (void)tableView:(UITableView *)theTableView commitEditingStyle:(UITableViewCellEditingStyle)editingStyle forRowAtIndexPath:(NSIndexPath *)indexPath I have all my logic for animating manipulated cells, removing from my model array etc. in this method. It is getting called when a user swipes, adds or rearranges, but I would like to call it manually/directly as a background thread changes my model. I have constructed an NSIndexPath like so: NSIndexPath *path = [NSIndexPath indexPathForRow:i inSection:1]; I just can't figure out how to call something like: [self.tableview commitEditingStyle:UITableViewCellEditingStyleDelete forRowAtIndexPath:path]; Do I need to gain access to the methods of this plain style UITableView in another way? Thanks:)

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  • Safe executing shell scripts; escaping vars before execution.

    - by Kirzilla
    Hello, Let's imagine that we have a simple php script that should get ssh_host, ssh_username, ssh_port from $_GET array and try to connect using this parameters to SSH. $port = escapeshellcmd($_GET['ssh_port']); $host = escapeshellcmd($_GET['ssh_host']); $username = escapeshellcmd($_GET['ssh_username']); $answer = shell_exec("ssh -p " . $port . " " . $user . "@" . $host); Is escapeshellcmd() enough or I need something more tricky? Or maybe I should use escapeshellarg() in this example? Thank you.

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  • Can an Excel VBA UDF called from the worksheet ever be passed an instance of any Excel VBA object mo

    - by jtolle
    I'm 99% sure that the answer is "no", but I'm wondering if someone who is 100% sure can say so. Consider a VBA UDF: Public Function f(x) End Function When you call this from the worksheet, 'x' will be a number, string, boolean, error, array, or object of type 'Range'. Can it ever be, say, an instance of 'Chart', 'ListObject', or any other Excel-VBA object model class? (The question arose from me moving to Excel 2007 and playing with Tables, and wondering if I could write UDFs that accept them as parameters instead of Ranges. The answer to that seems to be no, but then I realized I didn't know for sure in general.)

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  • formatting NSArray

    - by califguy
    So from the code below, I have managed to get the string *tempstring into an array chunk. Now chunk[0] contains 'a' while chunk[1] contains 'aa'. I am trying to format chunk[0] to '0a' which I can using the replaceObjectAtIndex method. Here's my question: How do I detect that chunk[0] is formatted as 'a' and not '0a'. I want to check all the indexes and make sure they have double digits and if not use a 0 to prefix it. NSString *tempstring = @"a-aa-bb"; NSMutableArray *chunk = [tempstring componentsSeparatedByString: @"-"]; NSLog(@"%@",[chunk objectAtIndex:0]);

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  • GA written in Java

    - by EnderMB
    I am attempting to write a Genetic Algorithm based on techniques I had picked up from the book "AI Techniques for Game Programmers" that uses a binary encoding and fitness proportionate selection (also known as roulette wheel selection) on the genes of the population that are randomly generated within the program in a two-dimensional array. I recently came across a piece of pseudocode and have tried to implement it, but have come across some problems with the specifics of what I need to be doing. I've checked a number of books and some open-source code and am still struggling to progress. I understand that I have to get the sum of the total fitness of the population, pick a random number between the sum and zero, then if the number is greater than the parents to overwrite it, but I am struggling with the implementation of these ideas. Any help in the implementation of these ideas would be very much appreciated as my Java is rusty.

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  • PHP pathinfo gets fooled by url in quert string. Any workaround?

    - by Majid
    I am working on a small function to take in a url and return a relative path based on where it resides itself. If the url contains a path in the query string, pathinfo returns incorrect results. This is demonstrated by the code below: $p = 'http://localhost/demos/image_editor/dir_adjuster.php?u=http://localhost/demos/some/dir/afile.txt'; $my_path_info = pathinfo($p); echo $p . '<br/><pre>'; print_r($my_path_info); echo '</pre>'; That code outputs: http://localhost/demos/image_editor/dir_adjuster.php?u=http://localhost/demos/some/dir/afile.txt Array ( [dirname] => http://localhost/demos/image_editor/dir_adjuster.php?u=http://localhost/demos/some/dir [basename] => afile.txt [extension] => txt [filename] => afile ) Which obviously is wrong. Any workaround?

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  • Dynamic programming: Find largest diamond (rhombus)

    - by Darksody
    I have a small program to do in Java. I have a 2D array filled with 0 and 1, and I must find the largest rhombus (as in square rotated by 90 degrees) and their numbers. Example: 0 1 0 0 0 1 1 0 1 1 1 0 1 0 1 1 1 1 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 Result: 1 1 1 1 1 1 1 1 1 1 1 1 1 The problem is similar to this SO question. If you have any idea, post it here.

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