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  • Imputing missing data in aligned sequences

    - by Kwame Oduro
    I want a simple perl script that can help me impute missing nucleotides in aligned sequences: As an example, my old_file contains the following aligned sequences: seq1 ATGTC seq2 ATGTC seq3 ATNNC seq4 NNGTN seq5 CTCTN So I now want to infer all Ns in the file and get a new file with all the Ns inferred based on the majority nucleotide at a particular position. My new_file should look like this: seq1 ATGTC seq2 ATGTC seq3 ATGTC seq4 ATGTC seq5 CTCTC A script with usage: "impute_missing_data.pl old_file new_file" or any other approach will be helpful to me. Thank you.

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  • two android threads and not synchronized data

    - by Sponge
    i have a (perhaps stupid) question: im using 2 threads, one is writing floats and one is reading this floats permanently. my question is, what could happen worse when i dont synchronize them? it would be no problem if some of the values would not be correct because they switch just a little every write operation. im running the application this way at the moment and dont have any problems so i want to know what could happen worse? a read/write conflict would cause a number like 12345 which is written to 54321 and red at the same time appear for example as 54345 ? or could happen something worse? (i dont want to use synchronization to keep the code as fast as possible)

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  • How to extract the lat/lng of pins in google maps?

    - by BCS
    I want to extract the latitude and longitude of a set of about 50-100 pins in a Google maps web page. I don't control the page and I don't need to do it more than once so I'm looking for something quick and dirty. I've got FireFox with FireBug as well as Chrome and all I need is something that's easier than re typing all the numbers.

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  • Where does User.Identity data come from?

    - by niaher
    For example: if I am retrieving User.Identity.Name, does it come from .ASPXAUTH cookie or is retrieved from the database using my membership provider? Are any database requests made when I access User.Identity? Thanks. EDIT: Right now I am pretty sure it comes from an authentication ticket cookie, but can't find any official documentation to confirm this. Anyone?

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  • Nested Data XML design

    - by esryl
    Looking to nest (to unlimited levels) elements in XML. Like so: <items> <item> <name>Item One</name> <item> <name>Item Two</name> </item> <item> <name>Item Three</name> <item> <name>Item Four</name> </item> <!-- etc... --> </item> </item> </items> However. While browsing for a solution I noticed in the comments of: http://stackoverflow.com/questions/988139/weird-nesting-in-xml while the above is well formed it would not validate against any sinsible DTD. Two things, what is a better way of nesting similar elements, and secondly what would be the design of the DTD. UPDATE: Would prefer to validate against an XML Schema rather than DTD.

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  • Python - from file to data structure?

    - by Seafoid
    Hi, I have large file comprising ~100,000 lines. Each line corresponds to a cluster and each entry within each line is a reference i.d. for another file (protein structure in this case), e.g. 1hgn 1dju 3nmj 8kfn 9opu 7gfb 4bui I need to read in the file as a list of lists where each line is a sublist, thus preserving the integrity of the cluster, e.g. nested_list = [['1hgn', '1dju', '3nmj', '8kfn'], ['9opu', '7gfb'], ['4bui']] My current code creates a nested list but the entries within each list are a single string and not comma separated. Therefore, I cannot splice the list with indices so easily. Any help greatly appreciated. Thanks, S :-)

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  • vs2010 Cache SQL data incorrect fields

    - by mickartz
    OK, I found a walkthrough on msdn for what I was after (offline database cache). However when I let the wizard create a local database from my online sql server the timespan fields are converted to a string?? Now I know the suggestion was to create my own local database and then use the MS Synch framework...however...this proclaims to do it "out of the box" However now I've a dataset which I've no idea how to use, and a database newly formed (for the synched cache) taht I will have to use Ling to Entities with(??) meanwhile I have this weird timespan to string conversion? should I give up now or push on? can i overwrite the the .designer.cs? typeof(string) to typeof(timespan)? damn wizards!!

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  • Altering ManagedObjects In NSArray

    - by Garry
    I have an entity called 'Job' with two boolean attributes named 'completed' and 'logged'. I am trying to retrieve all completed jobs that have not been logged at app start-up and change them to logged. I'm able to get all the completed but unlogged jobs with this fetchRequest: NSPredicate *predicate = [NSPredicate predicateWithFormat:@"(completed == %@ && logged == %@)", [NSNumber numberWithBool:YES], [NSNumber numberWithBool:NO]]; I'm then assigning this predicate to a fetchRequest and calling the [managedObjectContext executeFetchRequest:fetchRequest] method to get an array of all Job entities that meet this criteria. This seems to work fine and is returning the correct number of jobs. What I've been trying to do is loop through the NSArray returned, set the logged attribute to YES and then save. This seems to complete and doesn't return any errors but the changes are not persisted when the application quits. Where am I going wrong? [fetchRequest setPredicate:predicate]; NSError error; NSArray jobsToLog = [managedObjectContext executeFetchRequest:fetchRequest error:&error]; if ([jobsToLog count] > 0) { for (int i = 0; i < [jobsToLog count] - 1; i++) { [[jobsToLog objectAtIndex:i] setLogged:[NSNumber numberWithBool:YES]]; // Commit the changes made to disk error = nil; if (![managedObjectContext save:&error]) { // An error occurred } } } Thanks in anticipation,

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  • Using a comma seperated data in MYSQL "IN" clause

    - by Sashi Kant
    I have a column in one of my table where I store multiple ids seperated by comma's. Is there a way in which I can use this column's value in the "IN" clause of a query. The column(city) has values like 6,7,8,16,21,2 I need to use as Select * from table where e_ID in (Select city from locations where e_Id=?) I am satisfied with Crozin's answer, but I am open to suggestions, views and options. Feel free to share your views.

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  • Return XML data from a web service

    - by Nick LaMarca
    What is the best way to create a web service that returns a set of x,y coordinates? I am not sure on the object that is the best return type. When consuming the service I want to have it come back as xml preferibly something like this for example: <TheData> <Point> <x>0</x> <y>2</y> </Point> <Point> <x>5</x> <y>3</y> </Point> </TheData> If someone has a better structure to return please help I am new at all this.

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  • jsp error plz check this code why are not insert my data into database

    - by lekhni
    <%@ page language="java" import="java.util.*" pageEncoding="ISO-8859-1"%> <%@ page import="java.sql.*" %> <%@ page import="java.io.*"%> <%@ page import="java.io.File"%> <%@ page import="java.util.*"%> <%@ page import="java.sql.*"%> <%@ page import="java.sql.Blob"%> <%@ page import="java.sql.PreparedStatement"%> <%@ page import="java.sql.BatchUpdateException"%> <%@ page import="javax.servlet.*"%> <%@ page import="javax.servlet.http.*"%> <% String path = request.getContextPath(); String basePath = request.getScheme()+"://"+request.getServerName()+":"+request.getServerPort()+path+"/"; %> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <base href="<%=basePath%>"> <title>My JSP 'p.jsp' starting page</title> <meta http-equiv="pragma" content="no-cache"> <meta http-equiv="cache-control" content="no-cache"> <meta http-equiv="expires" content="0"> <meta http-equiv="keywords" content="keyword1,keyword2,keyword3"> <meta http-equiv="description" content="This is my page"> <!-- <link rel="stylesheet" type="text/css" href="styles.css"> --> </head> <body> <% int activityId = Integer.parseInt(request.getParameter("activityId")); String name = request.getParameter("name"); String activityType = request.getParameter("activityType"); int parentId = Integer.parseInt(request.getParameter("parentId")); String description = request.getParameter("description"); %> <% Connection conn=null; PreparedStatement pstatement = null; try{ Class.forName("com.mysql.jdbc.Driver"); conn=DriverManager.getConnection("jdbc:mysql://localhost:3306/pol","root","1234"); Statement st=conn.createStatement(); String queryString = "INSERT INTO activity(activityId,name,activityType,parentId,description)" + " VALUES (?, ?, ?, ?, ?)"; pstatement = conn.prepareStatement(queryString); pstatement.setInt(1, activityId); pstatement.setString(2, name); pstatement.setString(3, activityType); pstatement.setInt(4, parentId); pstatement.setString(5, description); } catch (Exception ex) { out.println("Unable to connect to batabase."); } finally { pstatement.close(); conn.close(); } %> </body> </html>

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  • Check for live Data Source Name Before proceeding

    - by n_kips
    Would it be ok to get a CF app to check for a valid database before proceeding to process that request? This is because there may be instances where the database server may be down or being upgraded, hence an error comes when a db dependant request is made. If there is no connection to the db server, the user can be safely redirected to a safe page. Or can cfcatch work? How can this check be done? Thank you.

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  • NSManagedObjectContext returns YES for hasChanges when there are none

    - by JK
    I created a separate NSManagedObjectContext on a separate thread to perform some store maintenance. However, I have noticed that the context returns YES for hasChanges as soon as a managed object in it is even referenced e.g. NSString *name = managedObject.name; This context is created and used exclusively in 1 method. Why is it returning has changes, when there there are none?

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  • Serial numbers generation without user data

    - by Sphynx
    This is a followup to this question. The accepted answer is generally sufficient, but requires user to supply personal information (e.g. name) for generating the key. I'm wondering if it's possible to generate different keys based on a common seed, in a way that program would be able to validate if those keys belong to particular product, but without making this process obvious to the end user. I mean it could be a hash of product ID plus some random sequence of characters, but that would allow user to guess potential new keys. There should be some sort of algorithm difficult to guess.

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  • write regex code in java for following data

    - by giri
    <table> <tr> <td style="width:180px"> <a href="/search?q=user:240698+[java]" class="post-tag" title="show all posts by this user in 'java'">java</a><span class="item-multiplier">&times;&nbsp;176</span><br> <a href="/search?q=user:240698+[servlets]" class="post-tag" title="show all posts by this user in 'servlets'">servlets</a><span class="item-multiplier">&times;&nbsp;25</span><br> <a href="/search?q=user:240698+[jsp]" class="post-tag" title="show all posts by this user in 'jsp'">jsp</a><span class="item-multiplier">&times;&nbsp;11</span><br> <a href="/search?q=user:240698+[core]" class="post-tag" title="show all posts by this user in 'core'">core</a><span class="item-multiplier">&times;&nbsp;9</span><br> </tr> </table> from the above code I need to fetch only java, servlets, jsp and core. Can anybody plz help me out to write a regex in java to fetch those? Thanks

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  • MATLAB: draw centroids

    - by Myx
    Hello - my main question is given a feature centroid, how can I draw it in MATLAB? In more detail, I have an NxNx3 image (an rgb image) of which I take 4x4 blocks and compute a 6-dimensional feature vector for each block. I store these feature vectors in an Mx6 matrix on which I run kmeans function and obtain the centroids in a kx6 matrix, where k is the number of clusters and 6 is the number of features for each block. How can I draw these center clusters in my image in order to visualize if the algorithm is performing the way I wish it to perform? Or if anyone has any other way/suggestions on how I can visualize the centroids on my image, I'd greatly appreciate it. Thank you.

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  • jquery.ui.tabs.js doesn't load tab data in IE9, Chrome - works perfectly fine in firefox

    - by Salma Khan
    I have few issues that I am facing on my site and I have no idea how to fix those. Please go to http://link.zambeel.ca/index.php/component/obituary/detail/52 and click on Photos tab, it doesn't load images promptly in IE9 and Chrome. I have made it work in firefox with the following code: var loadNextTab = function() { if (indexesToLoad.length == 0) return; var index = indexesToLoad.shift(); $("#tabs-1").tabs("load",index); }; $("#tabs-1").tabs({ cache: true, load: loadNextTab }); Please help me resolve this matter as soon as possible. Just to let you guys know, I am not a programmer by any means.

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  • What kind of good approaches use c++ programmers for storing error messages?

    - by Narek
    Say I have a huge code and have different kinds of error messages. For that I want to have a separate place where I store error codes and error messages. For example, for an error that occured because the program could not open a file I stroe: F001 "Can not open a file." "The same error message in another language" "The same error message in third language" What is the best way of storing different kind of error messages and codes in a file for c++ programmer in order to use that in a programme fast and easily? FYI I am working with Qt lib.

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