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• 50 sequences in one line

  - by user343934

  I have Muttiple sequence alignment (clustal) file and i want to read this file and arrange sequences in a such a way that in looks more clear and precise in order. I am doing this from biopython using AlignIO object. My codes like this alignment = AlignIO.read("opuntia.aln", "clustal") print "Number of rows: %i" % len(align) for record in alignment: print "%s - %s" % (record.id, record.seq) My Output-- http://i48.tinypic.com/ae48ew.jpg , it looks messy and long scrolling. What i want to do is print only 50 sequences in each line and continue till the end of alignment file. I wish to have output like this---http://i45.tinypic.com/4vh5rc.jpg from --http://www.ebi.ac.uk/Tools/clustalw2/, sorry two links are just a text due to my reputation. Any suggestions, algorithm and sample code is appreciated Thanks in advance Br,

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• Prolog - Finding the current directory, relative directory for 'tell' predicate

  - by Bharat

  I'm having trouble trying to figure out how to get prolog to spit out a text file where I want it to. I'm currently doing a bunch of operations and then using tell('output.txt') to record the output. Now the problem is that when I do this, it creates this file in the SWI \bin\ folder. I was wondering if there's a way to make it create this file in the directory containing the actual .pl file. So even if the file was moved (and it will be), the text file gets created right where the source file is. Long story short, is there a way to get the location of the source file once the source file has been consulted? Many Thanks!

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• Storing DateTime (UTC) vs. storing DateTimeOffset

  - by Frederico

  I usually have an "interceptor" that right before reading/writing from/to the database does datetime conversion (from UTC to localtime, and from localtime to utc), so I can use DateTime.Now (derivations and comparisions) throughout the system without worrying about timezones. Regarding serialization and moving data between computers, there is no need to bother, as the datetime is always UTC. Should I continue storing my dates (SQL 2008 - datetime) in UTC format or should I instead store it using DateTimeOffset (SQL 2008 - datetimeoffset)? UTC Dates in the database (datetime type) have been working and known for so long, why change it? What are the advantages? I have already looked into articles like this one, but I'm not 100% convinced though. Any thoughts?

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• R: How to pass a list of selection expressions (strings in this case) to the subset function?

  - by John

  Here is some example data: data = data.frame(series = c("1a", "1b", "1e"), reading = c(0.1, 0.4, 0.6)) > data series reading 1 1a 0.1 2 1b 0.4 3 1e 0.6 Which I can pull out selective single rows using subset: > subset (data, series == "1a") series reading 1 1a 0.1 And pull out multiple rows using a logical OR > subset (data, series == "1a" | series == "1e") series reading 1 1a 0.1 3 1e 0.6 But if I have a long list of series expressions, this gets really annoying to input, so I'd prefer to define them in a better way, something like this: series_you_want = c("1a", "1e") (although even this sucks a little) and be able to do something like this, subset (data, series == series_you_want) The above obviously fails, I'm just not sure what the best way to do this is?

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• Loading...Please wait for UIWebView - iPhone

  - by niha7229

  Hi guys, In Safari and other browsers, there is a bar that would indicate the percentage of the loading progress, and I, myself, trying to implement something similiar on iPhone, when loading some content in UIWebView, I would like the app to indicate the percentage of the page being loaded. I tried some google search and realize we could use NSURLConnection to read only the header and get the Content-Length ( but don't know how to, I read the Apple's NSURLConnection docs but probably I missed something ... ). And the size ( kb ) which UIWebView had loaded, seem like UIWebView don't support it for the public API... I hope this would be complete in some other ways than I thought, so if you have any ideas, please throw it out, thanks for your patient reading. P.S : I could just show an Activities Indicator for users with the long loading progress actions of the UIWebView but I just want to go further with the loading percentage bar :). Regards.

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• Fade animation UITableViewCell

  - by Tomas

  Hi everyone, I have a UITableViewController that populates a UITableView with some data that I pull off the net. The data for each cell consists also of an image used as background, which I'm downloading in a separated NSOperation added to a NSOperationQueue with a MaxConcurrentOperationCount set to 4. As long as the image is not downloaded I'm showing a generic placeholder which I would like to replace (fading out/fading in) with the downloaded image once it's being successfully downloaded. I'm using the following code placed inside the cellForRowAtIndexPath of the UITableViewController. [UIView beginAnimations:@"fade" context:nil]; [UIView setAnimationBeginsFromCurrentState:YES]; [UIView setAnimationDuration:3.0]; [UIView setAnimationCurve:UIViewAnimationCurveEaseInOut]; cell.placeholderUIImage.alpha = 0.0; cell.backgroundUIImage.alpha = 1.0; [UIView commitAnimations]; This is unfortunately just working randomly for a couple of rows, since for the most the background image is set instantly, as if the animation started on one cell would have been "overwritten" by the next call of beginAnimations.

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• How to run only the latest/a given test using Rspec?

  - by marcgg

  Let's say I have a big spec file with 20 tests because I'm testing a large model and I had no other way of doing it : describe Blah it "should do X" do ... end it "should do Y" do ... end ... it "should do Z" do ... end end Running a single file is faster than running the whole test suite, but it's still pretty long. Is there a way to run the last one (ie the one at the end of the file, here "should do Z")? If this is not possible, is there a way to specify which test I want to run in my file ?

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• Incremement Page Hit Count in Django

  - by Andrew C

  I have a table with an IntegerField (hit_count), and when a page is visited (ie. http://site/page/3) I want record id 3 'hit_count' column in the database to increment by 1. The query should be like: update table set hit_count = hit_count + 1 where id=3 Can I do this with the standard Django Model conventions? Or should I just write the query by hand? I'm starting a new project, so I am trying to avoid hacks. We'll see how long this lasts! Thanks!

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• jquery cookie - hoursToLive

  - by mathiregister

  Hi guys, i'm using the jquery cookie plugin. Everything works fine except the fact that I have no idea how to set an expiration-time for the cookie? $.cookie('opt_visible', 'true'); the jquery-cookie documentation says: hoursToLive (DEPRECATED for expiresAt) NUMBER For how many hours should the cookie be valid? (Passing 0 means to delete the cookie at the end of the browser session--this is default. Negative values will delete the cookie, but you should use the del() method instead.) That's exactly what I'd like to have. The cookie should be available as long as i'm browsing the site. As soon as i close the window or browsertab, the cookie should be deleted. How can i implement this hoursToLive thingy to my mentioned line above? Thank you

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• how to deploy jboss app over the internet

  - by james mccvoy

  I am using JBOSS 7 AS. I am deploying the projects via the linux box by the cmd like so bin/standalone.sh -b [ipaddress] This works fine only when i am on the network, however it doesn't work when i'm outside the network or over the internet. How do i launch it so people can access it over the internet? I tried this but it doesnt work. bin/standalone.sh -b 0.0.0.0 It says: Google Chrome could not load the webpage because took too long to respond. The website may be down, or you may be experiencing issues with your Internet connection.

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• What is the JVM Scheduling algorithm ?

  - by IHawk

  Hello ! I am really curious about how does the JVM work with threads ! In my searches in internet, I found some material about RTSJ, but I don't know if it's the right directions for my answers. I also found this topic in sun's forums, http://forums.sun.com/thread.jspa?forumID=513&threadID=472453, but that's not satisfatory. Can someone give me some directions, material, articles or suggestion about the JVM scheduling algorithm ? I am also looking for information about the default configurations of Java threads in the scheduler, like 'how long does it take for every thread' in case of time-slicing. And this stuff. I would appreciate any help ! Thank you !

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• How to force restart a Windows box using VBScript?

  - by tloach

  I'm trying to find a way to force Windows to reboot, and I am running into issues. I've tried Set OpSysSet = GetObject("winmgmts:{authenticationlevel=Pkt," _ & "(Shutdown)}").ExecQuery("select * from Win32_OperatingSystem where "_ & "Primary=true") for each OpSys in OpSysSet retVal = OpSys.Reboot() next I've also tried using the shutdown -f -r command, and in both cases I sometimes get no response, and if I try again I get an error saying "Action could not complete because the system is shutting down" even though no matter how long I leave it it doesn't shut down, it still allows me to start new programs, and doing a shutdown -a gives the same error. How can a script be used to force Windows to reboot?

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• GCC/XCode equivalent of _CrtCheckMemory?

  - by Chris Becke

  When dealing with random memory overwrites, in MSVC it is possible to validate the state of the heap at various points with a call to _CrtCheckMemory, and know with at least a small level of confidence that the code up until the check was not responsible for any errors that might cause new or malloc to fail later. In XCode, whats the equivalent way to try and box in a memory overwrite? All I have at the moment is a random failure of a call to new, somewhere deep in the bowels of some code with no real idea of how long the code has been running with a corrupt heap up until that point.

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• [Python] How do I read binary pickle data first, then unpickle it?

  - by conradlee

  I'm unpickling a NetworkX object that's about 1GB in size on disk. Although I saved it in the binary format (using protocol 2), it is taking a very long time to unpickle this file---at least half an hour. The system I'm running on has plenty of system memory (128 GB), so that's not the bottleneck. I've read here that pickling can be sped up by first reading the entire file into memory, and then unpickling it (that particular thread refers to python 3.0, which I'm not using, but the point should still be true in python 2.6). How do I first read the binary file, and then unpickle it? I have tried: import cPickle as pickle f = open("big_networkx_graph.pickle","rb") bin_data = f.read() graph_data = pickle.load(bin_data) But this returns: TypeError: argument must have 'read' and 'readline' attributes Any ideas?

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• How does Gmail do comet on Opera?

  - by Unknown

  I would like to know how Gmail (or anyone else) does comet on Opera. Here is what I know so far from my experiments. It doesn't use the event-source tag which is broken in Opera 10.51. It doesn't use iframe which displays a spinning throbber and a busy mouse cursor. It doesn't use responseText on xmlhttprequest when readyState = 3 which is known to be broken on Opera. I tried seeing how it was done in mibbit and etherpad, and I found that they both use long-polling.

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• Why Microsoft not provide for C# a static Win32 class with the most native functions and structures

  - by Oleg

  Everybody who used P/Invoke of Windows API knows a long list of declarations of static functions with attributes like [DllImport ("kernel32.dll", SetLastError = true, CharSet = CharSet.Auto)] The declaration of structures copied from Windows headers like WinNT.h or from web sites like www.pinvoke.net take also a lot of place in our programs. Why we all have to spend our time for this? Why Microsoft not give us a simple way to include a line like in old unmanaged programs #include <windows.h> and we would be have access to a static class Native with all or the most Windows functions and structures inside?

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• Grails: Querying Associations causes groovy.lang.MissingMethodException

  - by Paul

  Hi, I've got an issue with Grails where I have a test app with: class Artist { static constraints = { name() } static hasMany = [albums:Album] String name } class Album { static constraints = { name() } static hasMany = [ tracks : Track ] static belongsTo = [artist: Artist] String name } class Track { static constraints = { name() lyrics(nullable: true) } Lyrics lyrics static belongsTo = [album: Album] String name } The following query (and a more advanced, nested association query) works in the Grails Console but fails with a groovy.lang.MissingMethodException when running the app with 'run-app': def albumCriteria = tunehub.Album.createCriteria() def albumResults = albumCriteria.list { like("name", receivedAlbum) artist { like("name", receivedArtist) } // Fails here maxResults(1) } Stacktrace: groovy.lang.MissingMethodException: No signature of method: java.lang.String.call() is applicable for argument types: (tunehub.LyricsService$_getLyrics_closure1_closure2) values: [tunehub.LyricsService$_getLyrics_closure1_closure2@604106] Possible solutions: wait(), any(), wait(long), each(groovy.lang.Closure), any(groovy.lang.Closure), trim() at tunehub.LyricsService$_getLyrics_closure1.doCall(LyricsService.groovy:61) at tunehub.LyricsService$_getLyrics_closure1.doCall(LyricsService.groovy) (...truncated...) Any pointers?

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• Can I "inherit" a delegate? Looking for ways to combine Moq and MSpec without conflicts around It...

  - by Tomas Lycken

  I have started to use MSpec for BDD, and since long ago I use Moq as my mocking framework. However, they both define It, which means I can't have using Moq and using Machine.Specifications in the same code file without having to specify the namespace explicitly each time I use It. Anyone who's used MSpec knows this isn't really an option. I googled for solutions to this problem, and this blogger mentions having forked MSpec for himself, and implemented paralell support for Given, When, Then. I'd like to do this, but I can't figure out how to declare for example Given without having to go through the entire framework looking for references to Establish, and changing code there to match that I want either to be OK. For reference, the Establish, Because and It are declared in the following way: public delegate void Establish(); public delegate void Because(); public delegate void It(); What I need is to somehow declare Given, so that everywhere the code looks for an Establish, Given is also OK.

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• Programmatically create static arrays at compile time in C++

  - by Hippicoder

  One can define a static array at compile time as follows: const std::size_t size = 5; unsigned int list[size] = { 1, 2, 3, 4, 5 }; Question 1 - Is it possible by using various kinds of metaprogramming techniques to assign these values "programmatically" at compile time? Question 2 - Assuming all the values in the array are to be the same barr a few, is it possible to selectively assign values at compile time in a programmatic manner? eg: const std::size_t size = 7; unsigned int list[size] = { 0, 0, 2, 3, 0, 0, 0 }; Solutions using C++0x are welcome The array may be quite large, few hundred elements long The array for now will only consist of POD types It can also be assumed the size of the array will be known beforehand, in a static compile-time compliant manner. Solutions must be in C++ (no script or codegen based solutions)

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• PHP upload with progress bar

  - by Mitchan Adams

  Hi all I want to create an upload form to upload large files. Thats pretty much easy, however, the upload process itself taks long and basically looks like nothing is happening for a few minutes. So now I'd like to insert a progress bar to show the user that something is happening and they should just sit tight. I've read of numerous methods like APC and certian flash plugins, but my site is hosted on a shared server and I cant install any new applications on it. I'm thinking, maybe if it is possible to read the size of the temp file it creates via an ajax page. By polling the size every few seconds I should be able to get the progress of the upload. Now the question I pose is...where is the temp file situated?

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• Force line-buffering of stdout when piping to tee

  - by houbysoft

  Usually, stdout is line-buffered. In other words, as long as your printf argument ends with a newline, you can expect the line to be printed instantly. This does not appear to hold when using a pipe to redirect to tee. I have a C++ program, a, that outputs strings, always \n-terminated, to stdout. When it is run by itself (./a), everything prints correctly and at the right time, as expected. However, if I pipe it to tee (./a | tee output.txt), it doesn't print anything until it quits, which defeats the purpose of using tee. I know that I could fix it by adding a fflush(stdout) after each printing operation in the C++ program. But is there a cleaner, easier way? Is there a command I can run, for example, that would force stdout to be line-buffered, even when using a pipe?

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• How to flush data in php and disconnect user but keep the script alive

  - by Rodrigo

  This is a trick question, while developing a php+ajax application i felt into some long queries, nothing wrong with them, but they could be done in background. I know that there's a way to just send a reply to user while throwing the real processing to another process by exec(), however it dosen't feels right for me, this might generate exploits and it's not pratical on making it compatible with virtual servers and cross platform. PHP offers the ob_* functions although they help on flushing the cache, but the user will keep connected until the script is running. I'm wondering if there's an alternate to exec to keep a script running after sending data to user and closing connection/thread with apache, or a less "dirty" way to have processing data sent to another script.

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• Exposing some live data on a website - New to ASP.NET, need guidelines

  - by Carlos

  I have a large .NET based system running within the company intranet, which allows winforms users to see some live calculated numbers and a custom winforms control drawn live (but not real-time). The Forms users can also affect the operation of the system. I would like to just show the live numbers on a website, along with the custom control. Nothing needs to come back from the web user, as the web app is meant to be just for monitoring. All the numbers can be calculated at the server. It's been a long time since I touched ASP.NET, and I need to know how to proceed. What are the steps in building and deploying such a website? Any caveats I need to look out for?

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• Longer Form Fields in Drupal

  - by Slinger Jansen

  I have a really silly problem that has cost me a load of time already. I have created a content template with a URL in there. When I look at the HTML code for it, I see a big fat "maxlength=256" in the form tag. I'd like to expand the length of this field, because my customer wishes to enter really long links (over 500 characters). Any idea how I can change it? When I do a generic search through the code I see so many occurences of 256, but the length might just as well be in the database somewhere. I have of course made the database field a longer varchar (1024 sounded poetic to me), so that's something I don't have to worry about. I think it's silly, but the customer's always right, as we know. I am using Drupal 6.14.

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• Have you ever turned-down morally questionable or unethical web work?

  - by louism

  i'm just wondering if you guys have ever had a situation where you were offered a web development project which you turned down because you felt it was unethical or morally questionable. i've only had this once. i was offered a contract to develop a website for a meat abattoir (i.e. slaughterhouse). what's the problem you may ask? i'm vegetarian. i know, it's not an egregious dilemma, but it just didn't seem right to me. i have a female graphic designer friend who declined to work on a sex toys website where she was working at the time. funny thing is, it wouldn't bother me to work on a porn site (as long as it wasn't anything shifty - e.g. dwarfs + donkeys, that sort of thing). anyone else ever had a similar experience?

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