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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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  • 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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  • 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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  • Can not issue data manipulation statements with executeQuery in java

    - by user225269
    I'm trying to insert records in mysql database using java, What do I place in this code so that I could insert records: String id; String name; String school; String gender; String lang; Scanner inputs = new Scanner(System.in); System.out.println("Input id:"); id=inputs.next(); System.out.println("Input name:"); name=inputs.next(); System.out.println("Input school:"); school= inputs.next(); System.out.println("Input gender:"); gender= inputs.next(); System.out.println("Input lang:"); lang=inputs.next(); Class.forName("com.mysql.jdbc.Driver"); Connection con = DriverManager.getConnection("jdbc:mysql://localhost:3306/employee_record", "root", "MyPassword"); PreparedStatement statement = con.prepareStatement("insert into employee values('id', 'name', 'school', 'gender', 'lang');"); statement.executeUpdate();

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  • How do I remove the leaves of a binary tree?

    - by flopex
    I'm trying to remove all of the leaves. I know that leaves have no children, this is what I have so far. public void removeLeaves(BinaryTree n){ if (n.left == null && n.right == null){ n = null; } if (n.left != null) removeLeaves(n.left); if (n.right != null) removeLeaves(n.right); }

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  • MySQL move data from one table to another, matching ID's

    - by Reveller
    I have (a.o.) two MySQL tables with (a.o.) the following columns: tweets: ------------------------------------- id text from_user_id from_user ------------------------------------- 1 Cool tweet! 13295354 tradeny 2 Tweeeeeeeet 43232544 bolleke 3 Yet another 13295354 tradeny 4 Something.. 53546443 janusz4 users: ------------------------------------- id from_user num_tweets from_user_id ------------------------------------- 1 tradeny 2235 2 bolleke 432 3 janusz4 5354 I now want to normalize the tweets table, replacing tweets.from_user with an integer that matches users.id. Secondly, I want to fill in the corresponding users.from_user_id, Finally, I want to delete tweets.from_user_id so that the end result would look like: tweets: ------------------------ id text from_user ------------------------ 1 Cool tweet! 1 2 Tweeeeeeeet 2 3 Yet another 1 4 Something.. 3 users: ------------------------------------- id from_user num_tweets from_user_id ------------------------------------- 1 tradeny 2235 13295354 2 bolleke 432 43232544 3 janusz4 5354 53546443 My question is whether one could help me form the proper queries for this. I have only come so far: UPDATE tweets SET from_user = (SELECT id FROM users WHERE from_user = tweets.from_user) WHERE... UPDATE users SET from_user_id = (SELECT from_user_id FROM tweets WHERE from_user = tweets.from_user) WHERE... ALTER TABLE tweets DROP from_user_id Any help would be greatly appreciated :-)

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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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  • IndexOutOfRangeException when a stream is a multiple of the buffer size

    - by dnord
    I don't have a lot of experience with streams and buffers, but I'm having to do it for a project, and I'm stuck on an exception being thrown when the stream I'm reading is a multiple of the buffer size I've chosen. Let me show you: My code starts by reading bufferSize (100, let's say) bytes from the stream: numberOfBytesRead = DataReader.GetBytes(0, index, output, 0, bufferSize); Then, I loop through a while loop: while (numberOfBytesRead == bufferSize) { BufferWriter.Write(output); BufferWriter.Flush(); index += bufferSize; numberOfBytesRead = DataReader.GetBytes(0, index, output, 0, bufferSize); } ... and, once we get to a non-bufferSize read, we know we've hit the end of the stream and can move on. But if the bufferSize is 100, and the stream is 200, we'll read positions 0-99, 100-199, and then the attempt to read 200-299 errors out. I'd like it if it returned 0, but it throws an error. What I'm doing to handle that is, well, a try-catch: catch (System.IndexOutOfRangeException) numberOfBytesRead = 0; ...which ends the loop, and successfully finishes the thing, but we all know I don't want to control code flow with error handling. Is there a better (more standard?) way to handle stream reading when the stream length is unknown? This seems like a small wrinkle in a fairly reasonable strategy for reading streams, but I just don't know if I've got it wrong or what. The specifics of this (which I've cleaned up a little bit for posting) are a MySqlDataReader hitting a LARGEBLOB column. It's working whenever the buffer is larger than the number of returned bytes, or when the number of returned bytes is not a multiple of bufferSize. Because we don't, in that case, throw an IndexOutOfRangeException.

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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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  • When does it make sense to use a map?

    - by kiwicptn
    I am trying to round up cases when it makes sense to use a map (set of key-value entries). So far I have two categories (see below). Assuming more exist, what are they? Please limit each answer to one unique category and put up an example. Property values (like a bean) age -> 30 sex -> male loc -> calgary Presence, with O(1) performance peter -> 1 john -> 1 paul -> 1

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  • HTML forms and passing data back

    - by coLOLtip
    My html form is spreading over several pages (steps), and I want to let the use to take step back in case they would like to change something they filled in. So, I don't want to make users re-type all the information they already have typed once. Thus, how would I make it so that all the information would go back, to speak so? (I use PHP on server-side.)

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  • How to duplicate INSERTS into a seperate table?

    - by Ash
    An iPhone application I have installed uses an SQLite database to log entries with basic INSERTS and DELETES being performed on it. However I wish to keep a permanent log of the INSERTS made to this table, so when an INSERT occurs, I want it to be written to another table also as to create a log. I don't have access to the application source code in order to modify the SQL statements made, I do have access to the SQLite database. Can I do this with triggers? If so can somebody provide a short example.

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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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  • heirarchial data from self referencing table in tree form

    - by Beta033
    Ii looks like this has been asked and answered in all the simple cases, excluding the one that i'm having trouble with. I've tried using a recursive CTE to generate this, however maybe a cursor would be better? or maybe a set of recursive functions will do the trick? Can this be done in a cte? consider the following table PrimaryKey ParentKey 1 NULL 2 1 3 6 4 7 5 2 6 1 7 NULL should yield PK 1 -2 --5 -6 --3 7 -4 where the number of - marks equal the depth, my primary difficulty is the ordering.

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  • Tag Cloud Data Backend

    - by Waldron
    I want to be able to generate tag clouds from free text that comes from any number of different sources. For clarity, I'm not talking about how to display a tag cloud once the critical tags/phrases are already discovered, I'm hoping to be able to discover the meaningful phrases themselves... preferable on a PHP/MySQL stack. If I had to do this myself, I'd start by establishing some kind of index for words/phrases that gives a "normal" frequency for any word/phrase. eg "Constantinople" occurs once in every 1,000,000 words on average (normal frequency "0.000001"). Then as I analyze a body of text, I'd find the individual words/phrases (another challenge!), find frequencies of each within the input, and measure against the expected freqeuncy. Words that have the highest ratio against expected frequency get boosted priority in the cloud. I'd like to believe someone else has already done this, WAY better than I could hope to, but I'll be damned if I can find it. Any recommendations??

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  • How to bind a ComboBox to generic dictionary with xaml code

    - by MMD MNC
    I'm using the following code : private Dictionary<string, string> GetNumber { get; set; } public ReportsLetterTra() { GetMonth = new Dictionary<string, string> { {"1", "First"}, {"2", "Second"} }; InitializeComponent(); } xaml code : <ComboBox DisplayMemberPath="value" SelectedValuePath="key" ItemsSource="{Binding ElementName=reportslettra,Path=GetNumber}" SelectedIndex="0" Name="cmbFromNumber" /> Why is not bind GetNumber to cmbFromNumber?!

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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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  • Basic data alignment question

    - by Broken Logic
    I've been playing around to see how my computer works under the hood. What I'm interested in is seeing is what happens on the stack inside a function. To do this I've written the following toy program: #include <stdio.h> void __cdecl Test1(char a, unsigned long long b, char c) { char c1; unsigned long long b1; char a1; c1 = 'b'; b1 = 4; a1 = 'r'; printf("%d %d - %d - %d %d Total: %d\n", (long)&b1 - (long)&a1, (long)&c1 - (long)&b1, (long)&a - (long)&c1, (long)&b - (long)&a, (long)&c - (long)&b, (long)&c - (long)&a1 ); }; struct TestStruct { char a; unsigned long long b; char c; }; void __cdecl Test2(char a, unsigned long long b, char c) { TestStruct locals; locals.a = 'b'; locals.b = 4; locals.c = 'r'; printf("%d %d - %d - %d %d Total: %d\n", (long)&locals.b - (long)&locals.a, (long)&locals.c - (long)&locals.b, (long)&a - (long)&locals.c, (long)&b - (long)&a, (long)&c - (long)&b, (long)&c - (long)&locals.a ); }; int main() { Test1('f', 0, 'o'); Test2('f', 0, 'o'); return 0; } And this spits out the following: 9 19 - 13 - 4 8 Total: 53 8 8 - 24 - 4 8 Total: 52 The function args are well behaved but as the calling convention is specified, I'd expect this. But the local variables are a bit wonky. My question is, why wouldn't these be the same? The second call seems to produce a more compact and better aligned stack. Looking at the ASM is unenlightening (at least to me), as the variable addresses are still aliased there. So I guess this is really a question about the assembler itself allocates the stack to local variables. I realise that any specific answer is likely to be platform specific. I'm more interested in a general explanation unless this quirk really is platform specific. For the record though, I'm compiling with VS2010 on a 64bit Intel machine.

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  • Big-O for GPS data

    - by HH
    A non-critical GPS module use lists because it needs to be modifiable, new routes added, new distances calculated, continuos comparisons. Well so I thought but my team member wrote something I am very hard to get into. His pseudo code int k =0; a[][] <- create mapModuleNearbyDotList -array //CPU O(n) for(j = 1 to n) // O(nlog(m)) for(i =1 to n) for(k = 1 to n) if(dot is nearby) adj[i][j]=min(adj[i][j], adj[i][k] + adj[k][j]); His ideas transformations of lists to tables His worst case time complexity is O(n^3), where n is number of elements in his so-called table. Exception to the last point with Finite structure: O(mlog(n)) where n is number of vertices and m is an arbitrary constants Questions about his ideas why to waste resources to transform constantly-modified lists to table? Fast? only point where I to some extent agree but cannot understand the same upper limits n for each for-loops -- perhaps he supposed it circular why does the code take O(mlog(n)) to proceed in time as finite structure? The term finite may be wrong, explicit?

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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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  • 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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  • minLength data validation is not working with Auth component for CakePHP

    - by grokker
    Let's say I have a user registration and I'm using the Auth component (/user/register is allowed of course). The problem is if I need to set a minLength validation rule in the model, it doesn't work since the Auth component hashes the password therefore it's always more than my minlength password and it passes even if it's blank. How do I fix this issue? Thanks in advance!

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  • Tree-like queues

    - by Rehno Lindeque
    I'm implementing a interpreter-like project for which I need a strange little scheduling queue. Since I'd like to try and avoid wheel-reinvention I was hoping someone could give me references to a similar structure or existing work. I know I can simply instantiate multiple queues as I go along, I'm just looking for some perspective by other people who might have better ideas than me ;) I envision that it might work something like this: The structure is a tree with a single root. You get a kind of "insert_iterator" to the root and then push elements onto it (e.g. a and b in the example below). However, at any point you can also split the iterator into multiple iterators, effectively creating branches. The branches cannot merge into a single queue again, but you can start popping elements from the front of the queue (again, using a kind of "visitor_iterator") until empty branches can be discarded (at your discretion). x -> y -> z a -> b -> { g -> h -> i -> j } f -> b Any ideas? Seems like a relatively simple structure to implement myself using a pool of circular buffers but I'm following the "think first, code later" strategy :) Thanks

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