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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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  • 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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  • 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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  • Removing Redundant Data from a List<T>

    - by Mark
    I have a List of objects which are ordered. I would like to remove redundant objects where redundant does not necessarily mean duplicate. Here is an example: List<Point> points = new List<Point> { new Point(0, 10), new Point(1, 12), new Point(2, 16), new Point(3, 16), new Point(4, 16), new Point(5, 13), new Point(6, 16), }; I am interested in removing the new Point(3, 16) entry because it doesn't provide useful information; I already know that the element at 2=16 and the element at 4=16. The information that 3=16 doesn't do me any good in my application (because I already have the bounds {2,4}=16), so I would like to remove that entry. I'd also like to not that I want to keep the 5th and 6th entry because there are not consecutive entries where Y=16. Is there a slick way to do this with linq?

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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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  • 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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  • implementation of a queue using a circular array

    - by matin1234
    Hi I have found these algorithms in the internet but I can not understand that why in the enqueue method we compare size with N-1??? please help me thanks!! Algorithm size(): return (N-f+r)mod N Algorithm enqueue(e): if size()=N-1 then throw a FullQueueException Q[r]<---e r<----(r+1)mod N

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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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  • how to sort xml data in jQuery

    - by pixeltocode
    how can i sort all officers based on their ranks jQuery $.get('officers.xml', function(grade){ $(grade).find('officer').each(function(){ var $rank = $(this).attr('rank'); }); }); XML (officer.xml) <grade> <officer rank="2"></student> <officer rank="3"></student> <officer rank="1"></student> </grade> thanks.

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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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  • Python method to remove iterability

    - by Debilski
    Suppose I have a function which can either take an iterable/iterator or a non-iterable as an argument. Iterability is checked with try: iter(arg). Depending whether the input is an iterable or not, the outcome of the method will be different. Not when I want to pass a non-iterable as iterable input, it is easy to do: I’ll just wrap it with a tuple. What do I do when I want to pass an iterable (a string for example) but want the function to take it as if it’s non-iterable? E.g. make that iter(str) fails.

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  • Re-load Android activity data

    - by rhinds
    Hi, I am writing an Android app, part of which will be a survey involving multiple pages of checkbox question and answers. I have created an activity to display the question and options (from the DB) and what I want to do now is when i press the "Next" button it should just reload the current activity with the next question set from the database. (the activity starts with survey.getNextQuestion() - so its just a case of refreshing the activity so it updates) Im sure this is a simple thing to do -any ideas? Thanks

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  • CoreData is saving model without the save: method being called

    - by chris
    I have a list of items with a plus button in the navigation bar that opens up a modal window containing a table of the models attributes, that displays a form when the table items are clicked (pretty standard form style). For some reason if I click the plus button to open the form to create a new model, then immediately click the done button, the person model is saved. The action linked to the done button does nothing but call on a delegate method notifying the personListViewController to close the window. The apple docs do state that the model is not saved after calling the insertNewObjectForEntityName: ... Simply creating a managed object does not cause it to be saved to a persistent store. The managed object context acts as a scratchpad. I am at a lost to why this is happening, but every time I click the done button I have a new blank item in the original tableView. I am using SDK v3.1.3 // PersonListViewController - open modal window - (void)addPerson { // Load the new form PersonNewViewController *newController = [[PersonNewViewController alloc] init]; newController.modalFormDelegate = self; [self presentModalViewController:newController animated:YES]; [newController release]; } // PersonFormViewController - (void)viewDidLoad { [super viewDidLoad]; if ( person == nil ) { MyAppDelegate *appDelegate = [[UIApplication sharedApplication] delegate]; self.person = [NSEntityDescription insertNewObjectForEntityForName:@"Person" inManagedObjectContext:appDelegate.managedObjectContext]; } ... UIBarButtonItem *doneButton = [[UIBarButtonItem alloc] initWithBarButtonSystemItem:UIBarButtonSystemItemDone target:self action:@selector(done)]; self.navigationItem.rightBarButtonItem = doneButton; [doneButton release]; } - (IBAction) done { [self.modalFormDelegate didCancel]; } // delegate method in the original listViewController - (void) didCancel { [self dismissModalViewControllerAnimated:YES]; }

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  • What techniques are available for filtering collections of objects when using zodb?

    - by Omega
    As the title says: What techniques are available for filtering objects when using zodb? The equivalent in SQL terms would be something like filtering results by a date range. Or only returning rows with a particular value set in a column. If I had a series of blog posts and only wanted ones done in the past month, what would I have to do? Is there any way to optimize these kinds of "queries"? My gut tells me iterating over all the objects in a relationship simply to perform a test is less than optimal.

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  • Import part with specific meta data using MEF Preview 5

    - by Riri
    I have a export defined as as follows in MEF preview 5 [ExportMetadata("Application", "CheckFolderApplication")] [Export(typeof(ExtendedArtifactBase))] public class CheckFolderArtifact2 : ExtendedArtifactBase { ... Then I only want those imports with the "Application" "CheckFolderApplication" metadata. To currenly do that I read all the imports and then filter the result. [Import(typeof(ExtendedApplicationBase))] private ExportCollection<IApplication> _applications { get; set; } public IApplication GetApplication(string applicationName) { return _applications.Single(a => a.GetExportedObject().Name == applicationName).GetExportedObject(); } This feels really inefficient. What if I have thousands of plug-ins - do I have to read them all via MEF to just get one with the right metadata? If so how do you cache the result?

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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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  • Mysql: create index on 1.4 billion records

    - by SiLent SoNG
    I have a table with 1.4 billion records. The table structure is as follows: CREATE TABLE text_page ( text VARCHAR(255), page_id INT UNSIGNED ) ENGINE=MYISAM DEFAULT CHARSET=ascii The requirement is to create an index over the column text. The table size is about 34G. I have tried to create the index by the following statement: ALTER TABLE text_page ADD KEY ix_text (text) After 10 hours' waiting I finally give up this approach. Is there any workable solution on this problem? UPDATE: the table is unlikely to be updated or inserted or deleted. The reason why to create index on the column text is because this kind of sql query would be frequently executed: SELECT page_id FROM text_page WHERE text = ?

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  • Weird IF THAN not working with Requested data from URL text problem

    - by StealthRT
    Hey all, i am checking for an internet connection by checking for a file on my server. The file only has the word LIVE displayed on the page. No HTML or anything else is there, just the word LIVE. When i run this code, i do get the NSLog as saying "LIVE" but once i go to check it with the IF statement, it fails and i just do not know why??? NSString* myFile = [NSString stringWithFormat:@"http://www.xxx.com/iPodTouchPing.html"]; NSString* myFileURLString = [myFile stringByReplacingPercentEscapesUsingEncoding:NSASCIIStringEncoding]; NSData *myFileData = [[NSData alloc] initWithContentsOfURL:[NSURL URLWithString:myFileURLString]]; NSString *returnedMyFileContents=[[[NSString alloc] initWithData:myFileData encoding:NSASCIIStringEncoding] autorelease]; NSLog(@"%@", connected); if (connected == @"LIVE") { ... What am i doing wrong? I can not seem to find the reason?? David

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  • Oracle: Is there a way to get the column data types for a view?

    - by rally25rs
    For a table in oracle, I can query "all_tab_columns" and get table column information, like the data type, precision, whether or not the column is nullable. In SQL Developer or TOAD, you can click on a view in the GUI and it will spit out a list of the columns that the view returns and the same set of data (data type, precision, nullable, etc). So my question is, is there a way to query this column definition for a view, the way you can for a table? How do the GUI tools do it?

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  • ServerVariables and POST Data

    - by tyndall
    I've got a piece of tracking code which is capturing REMOTE_HOST, SERVER, REQUEST_METHOD, SCRIPT_NAME and QUERY_STRING. It grabs these from ServerVariables and sticks them in a database by user and IP. What is the best way to pick up the exact contents of what was posted back to a URL in ASP.NET? Is there an HTTP_POST? I'd rather not grab something and then have to parse it.

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  • Convert.ToSingle() for float data Type

    - by Asim Sajjad
    I have used many of the Convert.To..... functions for conversion , but I didn't understand one thing that for every datatype they have provide a Convert.To function but not for float datatype, in order to convert to float you need to use Convert.ToSingle() , why is this so ?

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