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  • How can I save BioPerl sequence nested features in genbank or embl format?

    - by Ryan Thompson
    In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that are concatenated to form the full coding sequence. However, when I use BioPerl to write a sequence object to a file in genbank or embl format, only the top-level features are written to the file, not the sub-features nested within the top-level features. How can I store my subfeatures in sequence files? Should I just convert all my subfeatures into top-level features, and then reconstruct the tree structure next time I read in the sequence?

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  • Understanding top output in Linux

    - by Rayne
    Hi, I'm trying to determine the CPU usage of a program by looking at the output from Top in Linux. I understand that %us means userspace and %sy means system/kernel etc. But say I see 100%us. Does this mean that the CPU is really only doing useful work? What if a CPU is tied up waiting for resources that are not avaliable, or cache misses, would it also show up in the %us column, or any other column? Thank you.

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  • I want to embed my own video files in my page

    - by Vinu
    I used the following codes to embed my videos(swf and flv) in the following code with the player. But this is working fine in ie and not working in firefox. If anyone knows to correct this code for firefox too.. pls help me... <object type="application/x-shockwave-flash" width="400" height="350" wmode="transparent" data="flvplayer.swf?file=**video location**&autoStart=true"> <param name="movie" value="flvplayer.swf?file=**video location**&autoStart=true" /> <param name="wmode" value="transparent" /> </object>

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  • Example of ==, equals and hashcode in java

    - by Abhishek Jain
    Given this: String s1= new String("abc"); String s2= new String("abc"); String s3 ="abc"; System.out.println(s1==s3); System.out.println(s1==s2); System.out.println(s1.equals(s2)); System.out.println(s1.equals(s3)); System.out.println(s1.hashCode()); System.out.println(s2.hashCode()); System.out.println(s3.hashCode()); Output is: false false true true 96354 96354 96354 Here == is giving false for each object but hashcode for each String object is same. Why is it so?

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  • Zero-channel RAID for High Performance MySQL Server (IBM ServeRAID 8k) : Any Experience/Recommendation?

    - by prs563
    We are getting this IBM rack mount server and it has this IBM ServeRAID8k storage controller with Zero-Channel RAID and 256MB battery backed cache. It can support RAID 10 which we need for our high performance MySQL server which will have 4 x 15000K RPM 300GB SAS HDD. This is mission-critical and we want as much bandwidth and performance. Is this a good card or should we replace with another IBM RAID card? IBM ServeRAID 8k SAS Controller option provides 256 MB of battery backed 533 MHz DDR2 standard power memory in a fixed mounting arrangement. The device attaches directly to IBM planar which can provide full RAID capability. Manufacturer IBM Manufacturer Part # 25R8064 Cost Central Item # 10025907 Product Description IBM ServeRAID 8k SAS - Storage controller (zero-channel RAID) - RAID 0, 1, 5, 6, 10, 1E Device Type Storage controller (zero-channel RAID) - plug-in module Buffer Size 256 MB Supported Devices Disk array (RAID) Max Storage Devices Qty 8 RAID Level RAID 0, RAID 1, RAID 5, RAID 6, RAID 10, RAID 1E Manufacturer Warranty 1 year warranty

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  • Sql Server SMO connection timeout not working

    - by Uros Calakovic
    I have the following PowerShell code: function Get-SmoConnection { param ([string] $serverName = "", [int] $connectionTimeout = 0) if($serverName.Length -eq 0) { $serverConnection = New-Object ` Microsoft.SqlServer.Management.Common.ServerConnection } else { $serverConnection = New-Object ` Microsoft.SqlServer.Management.Common.ServerConnection($serverName) } if($connectionTimeout -ne 0) { $serverConnection.ConnectTimeout = $connectionTimeout } try { $serverConnection.Connect() $serverConnection } catch [system.Management.Automation.MethodInvocationException] { $null } } $connection = get-smoconnection "ServerName" 2 if($connection -ne $null) { Write-Host $connection.ServerInstance Write-Host $connection.ConnectTimeout } else { Write-Host "Connection could not be established" } It seems to work, except for the part that attempts to set the SMO connection timeout. If the connection is successful, I can verify that ServerConnection.ConnectTimeout is set to 2 (seconds), but when I supply a bogus name for the SQL Server instance, it still attempts to connect to it for ~ 15 seconds (which is I believe the default timeout value). Does anyone have experience with setting SMO connection timeout? Thank you in advance.

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  • Retrieving Gtk::Widget's relative position: get_allocation() doesn't work

    - by a-v
    I need to retrieve the position of a Gtk::Widget relative to its parent, a Gtk::Table. Most sources (e.g. http://library.gnome.org/devel/gtk-faq/stable/x642.html) say that one needs to call Gtk::Widget::get_allocation(). However, the returned Gtk::Allocation object always contains x = -1, y = -1, width = 1, height = 1. I have to note that this happens before the Gtk::Table object is actually exposed and rendered. A call to show_all_children() or check_resize(), which I would expect to recalculate child widget geometry, doesn't help. What am I doing wrong? Thanks in advance.

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  • Can't get custom error rendering to work in symfony 1.4

    - by hongkildong
    I'm tring to customize error rendering in my form according to this example. Here is my code: if ($this['message']->hasError()) { $error_msg = '<ul>'; foreach ($this['message']->getError() as $error) $error_msg .= "<li>$error</li>"; $error_msg .= '</ul>'; } return $error_msg; but when $this['message'] has error this code returns '<ul></ul>' so it seems foreach ($this['message']->getError() as $error) causes no iterations $this['message']->getError() returns sfValidatorError object - maybe something changed in symfony 1.4 and it isn't iterable anymore... At first I thought that all magic in that example happened because of object being placed in $error by iteration implements __toString() but it seems no iterations happens at all...

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  • Quick / Built-in method for detecting table change in SQL Server?

    - by the-locster
    Is there a quick and easy way of telling if a table has changed in SQL Server? (I'm using SQL Server 2005). Something like an incrementing ID somewhere that updates on each INSERT, DELETE or UPDATE that I can keep track of. I noticed there is a sys.objects.modify_date column for each table, but I don't think it's quite what I want because the docs say: Date the object was last modified by using an ALTER statement. If the object is a table or a view, modify_date also changes when a clustered index on the table or view is created or altered.

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  • Puppet master/agent basic setup

    - by lewap
    I'm trying to setup a basic puppet agent/master use-case with an agent server and a master. I've setup two servers with puppet and puppet master respectively. After the following setup of both servers: puppet master --no-daemonize --verbose puppet agent --test puppet cert --list to get the list, puppet cert --sign to sign it. puppet agent --test I get the message: err: Could not retrieve catalog from remote server: hostname was not match with the server certificate warning: Not using cache on failed catalog err: Could not retrieve catalog; skipping run err: Could not send report: hostname was not match with the server certificate What do I need to do in order to get the agent/master to be able to talk to each other?

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  • Stackoverflow Flair Facebook app error

    - by emre
    Just to lewt you know, what happened when I allowed the app in FB Fatal error: Uncaught exception 'FacebookRestClientException' with message 'Param assoc_time must be a number' in /home/content/r/e/j/rejun2000/html/fb_so/php/facebookapi_php5_restlib.php:2878 Stack trace: #0 /home/content/r/e/j/rejun2000/html/fb_so/php/facebookapi_php5_restlib.php(2544): FacebookRestClient-call_method('facebook.data.s...', Array) #1 /home/content/r/e/j/rejun2000/html/fb_so/utils.php(188): FacebookRestClient-data_setAssociation('uid_so_uid2', '616867493', '5004213880486') #2 /home/content/r/e/j/rejun2000/html/fb_so/utils.php(208): setSoUID('616867493', -1, Object(Facebook)) #3 /home/content/r/e/j/rejun2000/html/fb_so/index.php(26): updateProfileBox('616867493', -1, Object(Facebook)) #4 {main} thrown in /home/content/r/e/j/rejun2000/html/fb_so/php/facebookapi_php5_restlib.php on line 2878

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  • Chrome: Black Screen of Death

    - by davidsinjaya
    I dont know when it started to happen. The screen will turn into full black when a page include javascript (I think so). I cannot open Youtube videos, but I can still see the source code and the pointer to find links and buttons and I can hear the sound of video. I have tried to clear my cache and reinstalled to the latest version, but nothing seems work. Moreover, I have disabled the Pepperflash Player as well, but it did not help. This my chrome version Google Chrome 22.0.1229.79 (Official Build 158531) OS Windows WebKit 537.4 (@129177) JavaScript V8 3.12.19.11 Flash 11.3.31.331 Please help.

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  • Facebook doesn't work on computer, but work on mobile device, both use the same router

    - by sasa
    I have a very strange problem and I'm thinking that can be problem with dns or something similar, but not sure and don't know how to solve. My computer is connected to router and every site works fine except facebook (Chrome and Firefox). Chrome shows "Error 101 (net::ERR_CONNECTION_RESET): The connection was reset." But, on mobile device witch is connected to the same router facebook works fine (Fb application and Delphin browser). Pinging facebook works fine. Clearing cookies and cache didn't help. Also, I performed antivirus and antimalware scan and there is nothing. What can be a problem? Update: I'm also connect notebook on that wifi router, and on it works fine. nslookup facebook.com Server: UnKnown Address: 192.168.1.1 Non-authoritative answer: Name: facebook.com Addresses: 2a03:2880:2110:3f01:face:b00c:: 2a03:2880:10:1f02:face:b00c:0:25 2a03:2880:10:8f01:face:b00c:0:25 69.171.224.37 69.171.229.11 69.171.242.11 66.220.149.11 66.220.158.11

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  • Can't load flash code into page with jquery ajax

    - by Philip
    I am trying to load some flash banner code (from database) into a webpage using jquery ajax. It is all working when adding the flash code in code-behind but when I am trying to load it with ajax some flash banners make the complete website disappear and only shows the banner. I am using jQuery Ajax and the response is in html like: <div id="ads"> <object ... Flash code ... </object> </div> I am using .html() to add it to the page.

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  • How Can I Populate Default Form Data with a ManyToMany Field?

    - by b14ck
    Ok, I've been crawling google and Django documentation for over 2 hours now (as well as the IRC channel on freenode), and haven't been able to figure this one out. Basically, I have a model called Room, which is displayed below: class Room(models.Model): """ A `Partyline` room. Rooms on the `Partyline`s are like mini-chatrooms. Each room has a variable amount of `Caller`s, and usually a moderator of some sort. Each `Partyline` has many rooms, and it is common for `Caller`s to join multiple rooms over the duration of their call. """ LIVE = 0 PRIVATE = 1 ONE_ON_ONE = 2 UNCENSORED = 3 BULLETIN_BOARD = 4 CHILL = 5 PHONE_BOOTH = 6 TYPE_CHOICES = ( ('LR', 'Live Room'), ('PR', 'Private Room'), ('UR', 'Uncensored Room'), ) type = models.CharField('Room Type', max_length=2, choices=TYPE_CHOICES) number = models.IntegerField('Room Number') partyline = models.ForeignKey(Partyline) owner = models.ForeignKey(User, blank=True, null=True) bans = models.ManyToManyField(Caller, blank=True, null=True) def __unicode__(self): return "%s - %s %d" % (self.partyline.name, self.type, self.number) I've also got a forms.py which has the following ModelForm to represent my Room model: from django.forms import ModelForm from partyline_portal.rooms.models import Room class RoomForm(ModelForm): class Meta: model = Room I'm creating a view which allows administrators to edit a given Room object. Here's my view (so far): def edit_room(request, id=None): """ Edit various attributes of a specific `Room`. Room owners do not have access to this page. They cannot edit the attributes of the `Room`(s) that they control. """ room = get_object_or_404(Room, id=id) if not room.is_owner(request.user): return HttpResponseForbidden('Forbidden.') if is_user_type(request.user, ['admin']): form_type = RoomForm elif is_user_type(request.user, ['lm']): form_type = LineManagerEditRoomForm elif is_user_type(request.user, ['lo']): form_type = LineOwnerEditRoomForm if request.method == 'POST': form = form_type(request.POST, instance=room) if form.is_valid(): if 'owner' in form.cleaned_data: room.owner = form.cleaned_data['owner'] room.save() else: defaults = {'type': room.type, 'number': room.number, 'partyline': room.partyline.id} if room.owner: defaults['owner'] = room.owner.id if room.bans: defaults['bans'] = room.bans.all() ### this does not work properly! form = form_type(defaults, instance=room) variables = RequestContext(request, {'form': form, 'room': room}) return render_to_response('portal/rooms/edit.html', variables) Now, this view works fine when I view the page. It shows all of the form attributes, and all of the default values are filled in (when users do a GET)... EXCEPT for the default values for the ManyToMany field 'bans'. Basically, if an admins clicks on a Room object to edit, the page they go to will show all of the Rooms default values except for the 'bans'. No matter what I do, I can't find a way to get Django to display the currently 'banned users' for the Room object. Here is the line of code that needs to be changed (from the view): defaults = {'type': room.type, 'number': room.number, 'partyline': room.partyline.id} if room.owner: defaults['owner'] = room.owner.id if room.bans: defaults['bans'] = room.bans.all() ### this does not work properly! There must be some other syntax I have to use to specify the default value for the 'bans' field. I've really been pulling my hair out on this one, and would definitely appreciate some help. Thanks!

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  • squid configuration change to accept http request on LAN

    - by Ratan Kumar
    installed squid + dansguardian to block adult content on my linux (ubuntu 12.10) . everything worked fine. it has blocked as expected . now the problem is i am also running an apache server for my LAN . ( kind of website ) but when accessing it via 192.168.0.1 , it says squid has blocked the connection , this is the exact error The following error was encountered while trying to retrieve the URL: http: //192.168.0.16/ Connection to 192.168.0.16 failed. The system returned: (113) No route to host The remote host or network may be down. Please try the request again. Your cache administrator is webmaster. before configuring the squid it was working fine . what changes in the squid.conf i have to make . i tried acl Safe_ports 80 allow_all Safe_ports ( i want to know how i can configure it again to listen HTTP request from LAN )

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  • Checking a set of listbox items against a text box vb.net

    - by Shane Fagan
    Hi all I have this code to check if an item from a textbox is in a listbox and its giving me the error at the bottom. Any ideas what im doing wrong? I copied it from another part of my project and it was working for that part so I cant see whats wrong. If LocationsSearchTextBox.Text <> "" And LocationListBox.Items.Count > 0 Then tempInt = 0 While (tempInt < ClientListBox.Items.Count) If LocationListBox.Items(tempInt).ToString.Contains(LocationsSearchTextBox.Text) = False Then LocationListBox.Items.RemoveAt(tempInt) End If tempInt += 1 End While End If System.ArgumentOutOfRangeException was unhandled Message="InvalidArgument=Value of '2' is not valid for 'index'. Parameter name: index" ParamName="index" Source="System.Windows.Forms" StackTrace: at System.Windows.Forms.ListBox.ObjectCollection.get_Item(Int32 index) at AuctioneerProject.Viewing.LocationsSearchTextBox_KeyPress(Object sender, KeyPressEventArgs e) in C:\Users\admin\Desktop\Auctioneers\AuctioneerProject\AuctioneerProject\Viewing.vb:line 301 at System.Windows.Forms.Control.OnKeyPress(KeyPressEventArgs e) at System.Windows.Forms.Control.ProcessKeyEventArgs(Message& m) at System.Windows.Forms.Control.ProcessKeyMessage(Message& m) at System.Windows.Forms.Control.WmKeyChar(Message& m) at System.Windows.Forms.Control.WndProc(Message& m) at System.Windows.Forms.TextBoxBase.WndProc(Message& m) at System.Windows.Forms.TextBox.WndProc(Message& m) at System.Windows.Forms.Control.ControlNativeWindow.OnMessage(Message& m) at System.Windows.Forms.Control.ControlNativeWindow.WndProc(Message& m) at System.Windows.Forms.NativeWindow.DebuggableCallback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam) at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg) at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(Int32 dwComponentID, Int32 reason, Int32 pvLoopData) at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context) at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context) at System.Windows.Forms.Application.Run(ApplicationContext context) at Microsoft.VisualBasic.ApplicationServices.WindowsFormsApplicationBase.OnRun() at Microsoft.VisualBasic.ApplicationServices.WindowsFormsApplicationBase.DoApplicationModel() at Microsoft.VisualBasic.ApplicationServices.WindowsFormsApplicationBase.Run(String[] commandLine) at AuctioneerProject.My.MyApplication.Main(String[] Args) in 17d14f5c-a337-4978-8281-53493378c1071.vb:line 81 at System.AppDomain._nExecuteAssembly(Assembly assembly, String[] args) at System.AppDomain.ExecuteAssembly(String assemblyFile, Evidence assemblySecurity, String[] args) at Microsoft.VisualStudio.HostingProcess.HostProc.RunUsersAssembly() at System.Threading.ThreadHelper.ThreadStart_Context(Object state) at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state) at System.Threading.ThreadHelper.ThreadStart() InnerException:

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  • How to read the response stream before the Http response completes

    - by Marwan Aouida
    When making a request using HttpWebRequest object, I need to call the method GetResponse() to send the request and get the response back. The problem with this method is that it doesn't return the response object until all data has been received. Say I am downloading a 100 MB file, I won't be able to read it until the response finish and all the 100 MB is downloaded. What I want is to be able to read the response stream bytes as soon as they arrive, without waiting for the response to complete. I know I can use the Range Http header, but it won't work on my situation.

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  • Entity Relationship Multiple 1:1's

    - by Evan
    I have an application where I have a generic object (table) called Hull. Each hull in the table is unique. I have another object that has three hulls, but they are specifically the Port_Hull, Center_Hull and Starboard_Hull. Rather than create a One to Many relationship, I was trying to create a one to one relationship for each one, but this results in numerous errors unless I make the relationship from Hull to Vessel one to many (which it is not). Any idea how I go about this, or should I abandon the concept and make the vessel to hull relationship one to many and deal with lists that always have three entries? p.s. Using uniqueidentifiers as many users can be adding records while disconnected. Hull Table HullID uniqueidentifier (primary key) plus bunch of hull data fields Vessel Table VesselID uniqueidentifier (primary key) MainHullID uniqueidentifier (tried as key and non-key) PortHullID uniqueidentifier StarboardHullID uniqueidentifier plus bunch of Vessel data fields

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  • Binding to static property

    - by Anthony Brien
    I'm having a hard time binding a simple static string property to a text box. Here's the class with the static property: public class VersionManager { private static string filterString; public static string FilterString { get { return filterString; } set { filterString = value; } } } In my xaml, I just want to bind this static property to a text box: <TextBox> <TextBox.Text> <Binding Source="{x:Static local:VersionManager.FilterString}"/> </TextBox.Text> </TextBox> Everything compiles, but at run time, I get the following exception: Cannot convert the value in attribute 'Source' to object of type 'System.Windows.Markup.StaticExtension'. Error at object 'System.Windows.Data.Binding' in markup file 'BurnDisk;component/selectversionpagefunction.xaml' Line 57 Position 29. Any idea what I'm doing wrong?

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  • Problem with running c# application on another PC

    - by draghia-aurelian
    I wrote a Windows Form Application in C# and it works well for my computer. But on another PC, an error occurs when i try to do some stuff. code 1 private void rUNToolStripMenuItem_Click(object sender, EventArgs e) { MessageBox.Show("I'm in rUNToolStripMenuItem_Click!"); ... } code 2 private void dataPositionToolStripMenuItem_Click(object sender, EventArgs e) { MessageBox.Show("I'm in dataPositionToolStripMenuItem_Click!"); ... } Running on my computer: code1: MessageBox appears! code2: MessageBox appears! Running on another computer: code1: MessageBox doesn't appear and the error happens! code2: MessageBox appears! The error is: Method not found: "Void Microsoft.CSharp.RuntimeBinder.CSharpGetMemberBider..ctor(System.String.System.Type, System.Collections.Generic.IEnumerable'1)'. This is the PrintScreen with error: Please help me to solve the problem!

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  • synchronized block in JSP tag class

    - by Sudhakar
    Hi, I am trying to find answer for the following ,for the past couple of days ,but couldnt find comprehensive answer Problem Statement I have a custom JSP tag class which handles a web form submission ,captures data and write it to same file in the filesystem. As all web applications,this can be triggeredsimultaneosly ,and i fear that multiple threads would be in action handling each of the submission (we all know thats how Servlet works.) CODE synchronized (this){ final String reportFileName = "testReport.csv"; File reportDir = new File( rootCsDirectory, "reports" ); if(!reportDir.isDirectory())reportDir.mkdir(); File reportFile = new File (reportDir, reportFileName); logReport(reportFile,reportContent.toString()); } ISSUE: - A File object can be opened by one thread for writing and at same time another thread might try to access and fail and throw an exception So i thought of synchronizing (on the object ) should solve the issue , but read some where that jsp engine would have pool of jsp tag objects, so i am afraid that synchronized (this) wont work and it should be changed to synchronized (this.getClass())

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  • How can I launch QuickTime from my app?

    - by Sheehan Alam
    I am trying to load a video from the web, but am having trouble getting it to appear in QuickTime. I can only hear the audio. I would like it to launch QuickTime. - (void)loadView { NSURL *movieURL = [NSURL URLWithString:@"http://movies.apple.com/media/us/mac/getamac/2009/apple-mvp-biohazard_suit-us-20090419_480x272.mov"]; if (movieURL != nil) { moviePlayer = [[MPMoviePlayerController alloc] initWithContentURL:movieURL]; moviePlayer.initialPlaybackTime = -1.0; // Register to receive a notification when the movie has finished playing. [[NSNotificationCenter defaultCenter] addObserver:self selector:@selector(moviePlayBackDidFinish:) name:MPMoviePlayerScalingModeDidChangeNotification object:moviePlayer]; [[NSNotificationCenter defaultCenter] addObserver:self selector:@selector(endPlay:) name:MPMoviePlayerPlaybackDidFinishNotification object:moviePlayer]; moviePlayer.scalingMode = MPMovieScalingModeAspectFit; moviePlayer.movieControlMode = MPMovieControlModeDefault; moviePlayer.backgroundColor = [UIColor blackColor]; [moviePlayer play]; } }

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  • Equivalent of describeType for Flex Component EVENTS

    - by Joshua
    Using "introspection" In Flex I can say: var classInfo:XML=describeType(SomeObject); Which will list for me the Accessors, Methods And Variables. (http://livedocs.adobe.com/flex/3/html/help.html?content=usingas_8.html) But what is the equivalent to programmatically inspect all of an object's possible EVENTS? (NOT JUST the events for which event listeners have been set, but to somehow step through a list of all VALID EVENTS for which event listeners may POTENTIALLY be set -- I realize that such lists are readily available online, and that's great for cases when I know the object's type at design type, but I require some way to inspect any given displayobject programmatically at runtime, and determine what events, if any, are or may be associated with it.)

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  • General rule - when to use a model (Codeigniter)

    - by pingu
    Hi guys, I was just curious as to what the rule of thumb was for models. Generally, I use them only for situations where I need to add/edit or update database entries for an object. However, I'm building an app at the moment that has a "config" table which holds various data, such as last updated, which will control when certain features in the app should be displayed. In this instance, I will mostly need to retrieve data from the config table. Is it worth putting these config methods in model? I'm interested to hear how more experienced coders approach the MVC methodology in CI - example pseudo methods (e.g., what methods relating to the same object you'd use in the model and the controller) would be most helpful.

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