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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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Zend_Session: unserialize session data

- by takeshin

I'm using session SaveHandler to persist session data in the database. Sample session_data column from the database: Messenger|a:1:{s:13:"page_messages";a:0:{}}userSession|a:1:{s:7:"referer";s:32:"http://cms.dev/user/profile/view";}Zend_Auth|a:1:{s:7:"storage";O:19:"User_Model_Identity":3:{s:2:"id";s:1:"1";s:8:"username";s:13:"administrator";s:4:"slug";s:13:"administrator";}} I want to delete Zend_Auth object from this session data. How can I unserialize those objects and remove object I need? I suspect, that I don't have to write my custom parser, that Zend_Session already has a method to do this. I have tried different combinations of unserialize but it still returns false. I'm using autoloader from ZF 1.10.2 and Doctrine 1.2

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How can I shift html-text in the JButton to the left?

- by Roman

I use HTML to put text into a JButton. In this way I can play with colors and text size. What I do not like is the distance from the left border of the button and the text (this separation is too large). Is there a way to decrease this distance? I think it should be some parameter in the style of the HTML code. Sample of the code: JButton btn = new JButton("<html><span style='color:#000000; font-size: 11pt;'>" + label + "</span></html>");

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Overriding constructors

- by demas

Here is sample code: class One def initialize(*args) case args.size when 0 puts "one initialize" when 1 puts "one initialize #{args[0]}" end end end class Two def initialize(*args) if args.size == 2 then puts "two initialize #{args[0]} and #{args[1]}" else super(args) end end end one = One.new one = One.new("thing") two = Two.new("some", "other") two = Two.new("some") Now I'm launching the code and getting the error message: [[email protected]][~/temp]% ruby test2.rb one initialize one initialize thing two initialize some and other test2.rb:17:in `initialize': wrong number of arguments(1 for 0) (ArgumentError) from test2.rb:17:in `initialize' from test2.rb:26:in `new' from test2.rb:26:in `<main>' How can I call parent's constructor from class Two ?

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Parsing html for domain links

- by Hallik

I have a script that parses an html page for all the links within it. I am getting all of them fine, but I have a list of domains I want to compare it against. So a sample list contains list=['www.domain.com', 'sub.domain.com'] But I may have a list of links that look like http://domain.com http://sub.domain.com/some/other/page I can strip off the http:// just fine, but in the two example links I just posted, they both should match. The first I would like to match against the www.domain.com, and the second, I would like to match against the subdomain in the list. Right now I am using url2lib for parsing the html. What are my options in completely this task?

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Core Animation bad access on device

- by user1595102

I'm trying to do a frame by frame animation with CAlayers. I'm doing this with this tutorial http://mysterycoconut.com/blog/2011/01/cag1/ but everything works with disable ARC, when I'm try to rewrite code with ARC, it's works on simulator perfectly but on device I got a bad access memory. Layer Class interface #import <Foundation/Foundation.h> #import <QuartzCore/QuartzCore.h> @interface MCSpriteLayer : CALayer { unsigned int sampleIndex; } // SampleIndex needs to be > 0 @property (readwrite, nonatomic) unsigned int sampleIndex; // For use with sample rects set by the delegate + (id)layerWithImage:(CGImageRef)img; - (id)initWithImage:(CGImageRef)img; // If all samples are the same size + (id)layerWithImage:(CGImageRef)img sampleSize:(CGSize)size; - (id)initWithImage:(CGImageRef)img sampleSize:(CGSize)size; // Use this method instead of sprite.sampleIndex to obtain the index currently displayed on screen - (unsigned int)currentSampleIndex; @end Layer Class implementation @implementation MCSpriteLayer @synthesize sampleIndex; - (id)initWithImage:(CGImageRef)img; { self = [super init]; if (self != nil) { self.contents = (__bridge id)img; sampleIndex = 1; } return self; } + (id)layerWithImage:(CGImageRef)img; { MCSpriteLayer *layer = [(MCSpriteLayer*)[self alloc] initWithImage:img]; return layer ; } - (id)initWithImage:(CGImageRef)img sampleSize:(CGSize)size; { self = [self initWithImage:img]; if (self != nil) { CGSize sampleSizeNormalized = CGSizeMake(size.width/CGImageGetWidth(img), size.height/CGImageGetHeight(img)); self.bounds = CGRectMake( 0, 0, size.width, size.height ); self.contentsRect = CGRectMake( 0, 0, sampleSizeNormalized.width, sampleSizeNormalized.height ); } return self; } + (id)layerWithImage:(CGImageRef)img sampleSize:(CGSize)size; { MCSpriteLayer *layer = [[self alloc] initWithImage:img sampleSize:size]; return layer; } + (BOOL)needsDisplayForKey:(NSString *)key; { return [key isEqualToString:@"sampleIndex"]; } // contentsRect or bounds changes are not animated + (id < CAAction >)defaultActionForKey:(NSString *)aKey; { if ([aKey isEqualToString:@"contentsRect"] || [aKey isEqualToString:@"bounds"]) return (id < CAAction >)[NSNull null]; return [super defaultActionForKey:aKey]; } - (unsigned int)currentSampleIndex; { return ((MCSpriteLayer*)[self presentationLayer]).sampleIndex; } // Implement displayLayer: on the delegate to override how sample rectangles are calculated; remember to use currentSampleIndex, ignore sampleIndex == 0, and set the layer's bounds - (void)display; { if ([self.delegate respondsToSelector:@selector(displayLayer:)]) { [self.delegate displayLayer:self]; return; } unsigned int currentSampleIndex = [self currentSampleIndex]; if (!currentSampleIndex) return; CGSize sampleSize = self.contentsRect.size; self.contentsRect = CGRectMake( ((currentSampleIndex - 1) % (int)(1/sampleSize.width)) * sampleSize.width, ((currentSampleIndex - 1) / (int)(1/sampleSize.width)) * sampleSize.height, sampleSize.width, sampleSize.height ); } @end I create the layer on viewDidAppear and start animate by clicking on button, but after init I got a bad access error -(void)viewDidAppear:(BOOL)animated { [super viewDidAppear:animated]; NSString *path = [[NSBundle mainBundle] pathForResource:@"mama_default.png" ofType:nil]; CGImageRef richterImg = [UIImage imageWithContentsOfFile:path].CGImage; CGSize fixedSize = animacja.frame.size; NSLog(@"wid: %f, heigh: %f", animacja.frame.size.width, animacja.frame.size.height); NSLog(@"%f", animacja.frame.size.width); richter = [MCSpriteLayer layerWithImage:richterImg sampleSize:fixedSize]; animacja.hidden = 1; richter.position = animacja.center; [self.view.layer addSublayer:richter]; } -(IBAction)animacja:(id)sender { if ([richter animationForKey:@"sampleIndex"]) {NSLog(@"jest"); } if (! [richter animationForKey:@"sampleIndex"]) { CABasicAnimation *anim = [CABasicAnimation animationWithKeyPath:@"sampleIndex"]; anim.fromValue = [NSNumber numberWithInt:0]; anim.toValue = [NSNumber numberWithInt:22]; anim.duration = 4; anim.repeatCount = 1; [richter addAnimation:anim forKey:@"sampleIndex"]; } } Have you got any idea how to fix it? Thanks a lot.

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JSF 2.0 Problem (faces-config)

- by Sarang

Hello everybody, We have faces-config.xml in JSF 1.0 where we entry about managed-beans, dependencies & navigations etc. I was developing a sample project using JSF 2.0. But, as I don't know annotation, I need to include face-config.xml externally. Please, provide the solution for it, as in JSF 2.0 we don't need to include it. What is reason behind it ? How do we set a bean as managed-bean. What is annotation ? How is it used ? Thanking you.

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datepicker common options but different altField altFormat

- by Legio X

Using jquery-ui datepicker I would like to use altField and altFormat to 2 datepickers on the same page but I can't figure out how to add these 2 options which are specific to each datepicker along with my common set of options. Code sample below. #dt1 does not work, but #dt2 works. How can I get #dt1 to work while using the datepickerOpts? var datepickerOpts = { minDate: -2, changeMonth: true, changeYear: true, dateFormat: 'yy-mm-dd' }; $('#dt1').datepicker(datepickerOpts, {altField: '#alt1', altFormat: 'mm-dd-yy' }); $('#dt2').datepicker({ minDate: -2, changeMonth: true, changeYear: true, dateFormat: 'yy-mm-dd', altField: '#alt2', altFormat: '@' });

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FF extension: displaying an array of string elements in a sidebar

- by sujay-jain

I am developing a ff extension which displays a list of elements from an array (dynamic) in the sidebar. The array is dynamic and needs to be constructed in a function everytime the sidebar is opened (or any other event handler). Later, i will need to implement link functionality on parts of the string. What is the best way to go about this? I have created an empty sidebar and just know the label element as of now. menu, and menuitem dont work. What other elements can i use to display text in a good way which supports dynamic contruction. Is there some good tutorial/sample extension which i can see and learn?

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.NET SerialPort.Read skipps bytes

- by Lukas Rieger

Solution Reading the data byte wise via "port.ReadByte" is too slow, the problem is inside the SerialPort class. i changed it to reading bigger chunks via "port.Read" and there are now no buffer overruns. although i found the solution myself, writing it down helped me and maybe someone else has the same problem and finds this via google... (how can i mark it as answered?) EDIT 2 by setting port.ReadBufferSize = 2000000; i can delay the problem for ~30 seconds. so it seems, .Net really is too slow... since my application is not that critical, i just set the buffer to 20MB, but i am still interested in the cause. EDIT i just tested something i had not thought of before (shame on me): port.ErrorReceived += (object self, SerialErrorReceivedEventArgs se_arg) => { Console.Write("| Error: {0} | ", System.Enum.GetName(se_arg.EventType.GetType(), se_arg.EventType)); }; and it seems that i have an overrun. Is the .Net implementation too slow for 500k or is there an error on my side? Original Question i built a very primitive oszilloscope (avr, which sends adc data over uart to an ftdi chip). On the pc side i have a WPF Programm that displays this data. The Protokoll is: two sync bytes (0xaffe) - 14 data bytes - two sync bytes - 14 data bytes - ... i use 16bit values, so inside the 14 data bytes are 7 channels (lsb first). I verified the uC Firmware with hTerm, and it does send and receive everything correct. But, if i try to read the data with C#, sometimes some bytes are lost. The oszilloscop programm is a mess, but i created a small sample application, which has the same symptoms. I added two extension methods to a) read one byte from the COM Port and ignore -1 (EOF) and b) wait for the sync pattern. The sample programm first syncs onto the data stream by waiting for (0xaffe) and then compares the received bytes with the expected values. the loop runs a few times until an assert failed message pops up. I could not find anything about lost bytes via google, any help would be appreciated. Code using System; using System.Collections.Generic; using System.Diagnostics; using System.IO.Ports; using System.Linq; using System.Text; using System.Threading.Tasks; namespace SerialTest { public static class SerialPortExtensions { public static byte ReadByteSerial(this SerialPort port) { int i = 0; do { i = port.ReadByte(); } while (i < 0 || i > 0xff); return (byte)i; } public static void WaitForPattern_Ushort(this SerialPort port, ushort pattern) { byte hi = 0; byte lo = 0; do { lo = hi; hi = port.ReadByteSerial(); } while (!(hi == (pattern >> 8) && lo == (pattern & 0x00ff))); } } class Program { static void Main(string[] args) { //500000 8n1 SerialPort port = new SerialPort("COM3", 500000, Parity.None, 8, StopBits.One); port.Open(); port.DiscardInBuffer(); port.DiscardOutBuffer(); //Sync port.WaitForPattern_Ushort(0xaffe); byte hi = 0; byte lo = 0; int val; int n = 0; // Start Loop, the stream is already synced while (true) { //Read 7 16-bit values (=14 Bytes) for (int i = 0; i < 7; i++) { lo = port.ReadByteSerial(); hi = port.ReadByteSerial(); val = ((hi << 8) | lo); Debug.Assert(val != 0xaffe); } //Read two sync bytes lo = port.ReadByteSerial(); hi = port.ReadByteSerial(); val = ((hi << 8) | lo); Debug.Assert(val == 0xaffe); n++; } } } }

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Home key press behaviour

- by Arnab

While developing a sample android application i have constructed two activities 1)Activity 1 2)Activity 2 Now Activity 2 is the foreground activity whereas Activity 1 is the background one. Now user presses Home key. The application(i.e. both the activities) dissappear. Now is we relaunch the application we see Activity 1 as the foreground activity. My question is: 1)Does the platform maintain any history entry when pressed home key? 2)How do we take the user to the last launch activity on relaunching the application?

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ShowDialog returns immediately after a handled exception in .net compact framework

- by leiz

The problem I am having is that for some reason ShowDialog returns immediately after handle an exception. However, it works for MessageBox.Show() or at the second time I call ShowDialog. What is the best workaround for this problem? I was only able to find this. And I cannot believe that no one else has this issue. I am using .net compact framework 3.5. Sample code: try { using(SomeForm f = new SomeForm()) { f.ShowDialog(); } } catch(SomeException) { using(SomeOtherForm f = new SomeOtherForm()) { f.ShowDialog(); // this returns immediately // if this is MessageBox.Show(), it works correctly. f.ShowDialog(); // then this works fine } }

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How to get a list of names + a count of occurrences relating to the name from another table

- by Jacob Degeling

Hi, Hope my subject line was descriptive enough. Basically, I have a table called Students, and one called Absences. The Students table contains student information (Name, DOB, StudentID etc.), the Absences table contains any absences (Date, Reason, related by StudentID). I want to get a full list of the students, plus a count of their absences. Sample results would be: StudentName Absences ------------- ----------- Johnny 3 Mark 2 James 1 Anthony 0 Sharon 0 Can someone suggest a way I should tackle this problem? I would prefer to have a single SQL statement, possibly incorporating some views etc. Thanks, Jacob.

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How to calculate a operation's time in micro second precision

- by Sanjeet Daga

I want to calculate performance of a function in micro second precision on Windows platform. Now Windows itself has milisecond granuality, so how can I achieve this. I tried following sample, but not getting correct results. LARGE_INTEGER ticksPerSecond = {0}; LARGE_INTEGER tick_1 = {0}; LARGE_INTEGER tick_2 = {0}; double uSec = 1000000; // Get the frequency QueryPerformanceFrequency(&ticksPerSecond); //Calculate per uSec freq double uFreq = ticksPerSecond.QuadPart/uSec; // Get counter b4 start of op QueryPerformanceCounter(&tick_1); // The ope itself Sleep(10); // Get counter after opfinished QueryPerformanceCounter(&tick_2); // And now the op time in uSec double diff = (tick_2.QuadPart/uFreq) - (tick_1.QuadPart/uFreq);

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With ASP .NET, how do I display a side submenu depending on what user picked from the main menu?

- by Ole Media

Hello, I come from PHP side, but I'm in need to develop a site using ASP .NET So far I manage to create a master page. Now I'm dealing with menus and submenus What I'm trying to do is, if the user picks "About Us" from the main menu, under the about us page I want to display a submenu with the options "who we are, what we do, contact us" If the user picks "Our Products" from the main menu, then under the products page I want to display a submenu with the options "product 1, product 2, product 3" Is this possible with only one master page? I read something about menu control but not sure that is what I need. So far I found how to display a sitemap, but not specific sections of a sitemap, if this is the way to do things. Any links, sample code, point of reference will be appreciated. Thanks

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openGL ES retina support

- by Bryan

I'm trying to get the avTouch sample code app to run on the retina display. Has anyone done this? In the CALevelMeter class, I've tried the following: - (id)initWithCoder:(NSCoder *)coder { if (self = [super initWithCoder:coder]) { CGFloat f = self.contentScaleFactor; if ([self respondsToSelector:@selector(contentScaleFactor)]) { self.contentScaleFactor = [[UIScreen mainScreen] scale]; } f = self.contentScaleFactor; _showsPeaks = YES; _channelNumbers = [[NSArray alloc] initWithObjects:[NSNumber numberWithInt:0], nil]; _vertical = NO; _useGL = YES; _meterTable = new MeterTable(kMinDBvalue); [self layoutSubLevelMeters]; [self registerForBackgroundNotifications]; } return self; } and it sets the contentScaleFactor to "2". Great, that was expected. But then in the layoutSubviews, CALevelMeter frame is still 1/2 of what it should be. Any ideas?

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How to get attribute of a model saved in instance variable

- by Nazar

I am writing a plugin, in which i define a new relation dynamically with in plugin. Sample code is given below module AttachDocumentsAs @as = nil def attach_documents_as(*attachment_as) attachment_as = attachment_as.to_a.flatten.compact.map(&:to_sym) @as = attachment_as.first class_inheritable_reader(@as) class_eval do has_many @as, :as => :attachable, :class_name=>"AttachDocuments::Models::AttachedDocument" accepts_nested_attributes_for @as end end end now in any model i used it as class Person < AtiveRecord::Base attach_documents_as :financial_documents end Now want to access want to access this attribute of the class in overloaded initialize method like this def initialize(*args) super(*args) "#{@as}".build end But it is not getting required attribute, can any one help me in it. I want to build this relation and set some initial values. Waiting for guidelines from all you guys.

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Help with a MySQL SELECT WHERE Clause

- by Dr. DOT

A column in my table contains email addresses. I have a text string that contains the a few usernames of email addresses separated by commas. I can make text sting into an array if necessary to get my SELECT WHERE clause to work correctly. Text string search argument is 'bob,sally,steve' I want to produce a WHERE clause that only returns rows where the username portion of the email address in the table matches one of the usernames in my text string search argument. Thus a row with [email protected] would not be returned but [email protected] would be. Does anyone have a WHERE clause sample that produces this result? Thanks.

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How to resolve Resharper's "unused property" warning on properties solely for Display/Value Members?

- by JYelton

I have defined two properties "Name" and "ID" for an object which I use for the DisplayMember and ValueMember of a ComboBox with a BindingList datasource. I recently installed Resharper to evaluate it. Resharper is giving me warnings on the object that the two properties are unused. Sample code: BindingList<ClassSample> SampleList = new BindingList<ClassSample>(); // populate SampleList cmbSampleSelector.DisplayMember = "Name"; cmdSampleSelector.ValueMember = "ID"; cmbSampleSelector.DataSource = SampleList; private class ClassSample { private string _name; private string _id; public string Name // Resharper believes this property is unused { get { return _name; } } public string ID // Resharper believes this property is unused { get {return _id; } } public ClassSample(string Name, string ID) { _name = Name; _id = ID; } } Am I doing something wrong or is Resharper clueless about this particular usage?

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Count word occurrences in a text field with LINQ

- by Yoann. B

How can i get the occurrences count of a Word in a database text field With LINQ ? Keyword token sample : ASP.NET EDIT 4 : Database Records : Record 1 : [TextField] = "Blah blah blah ASP.NET bli bli bli ASP.NET blu ASP.NET yop yop ASP.NET" Record 2 : [TextField] = "Blah blah blah bli bli bli blu ASP.NET yop yop ASP.NET" Record 3 : [TextField] = "Blah ASP.NET blah ASP.NET blah ASP.NET bli ASP.NET bli bli ASP.NET blu ASP.NET yop yop ASP.NET" So Record 1 Contains 4 occurrence of "ASP.NET" keyword Record 2 Contains 2 occurrence of "ASP.NET" keyword Record 3 Contains 7 occurrence of "ASP.NET" keyword Collection Extraction IList < RecordModel (ordered by word count descending) Record 3 Record 1 Record 2 LinqToSQL should be the best, but LinqToObject too :) NB : No issue about the "." of ASP.NET keyword (this is not the goal if this question)

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jQuery Validate - Require at least one from group, plus additional items.

- by Kevin Pullin

I'm attempting to use 'jQuery Validate' on a form that requires an email address plus either all items of a shipping address completed or none at all. Using the sample provided by the solution to this question: jQuery Validate - “Either skip these fields, or fill at least X of them”, I have been able to successfully solve the validation of the address group. The problem, however, is that the logic for validating the email address field does not work. From debugging the Validate scripts, the "re-entrant" validation code triggered by calling 'fields.data('being_validated', true).valid();' in the linked example results in a reset of all previously validated errors (i.e. the email validation error is cleared). I have modified some existing samples, the first in which removes the offending line and the second with it included. Email Validation Working Email Validation Fails Any tips or suggestions on how to properly solve this or work around the failure?

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Regular expression quantifier questions

- by Josemalive

Hello, Im trying to find a regular expression that matches this kind of URL: http://sub.domain.com/selector/F/13/K/100546/sampletext/654654/K/sampletext_sampletext.html and dont match this: http://sub.domain.com/selector/F/13/K/10546/sampletext/5987/K/sample/K/101/sample_text.html only if the number of /K/ is minimum 1 and maximum 2 (something with a quantifier like {1,2}) Until this moment i have the following regexp: http://sub\.domain\.com/selector/F/[0-9]{1,2}/[a-z0-9_-]+/ Now i would need a hand to add any kind of condition like: Match this if in the text appears the /K/ from 1 to 2 times at most. Thanks in advance. Best Regards. Josema

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removing a line from a text file?

- by Blackbinary

Hi all. I am working with a text file, which contains a list of processes under my programs control, along with relevant data. At some point, one of the processes will finish, and thus will need to be removed from the file (as its no longer under control). Here is a sample of the file contents (which has enteries added "randomly"): PID=25729 IDLE=0.200000 BUSY=0.300000 USER=-10.000000 PID=26416 IDLE=0.100000 BUSY=0.800000 USER=-20.000000 PID=26522 IDLE=0.400000 BUSY=0.700000 USER=-30.000000 So for example, if I wanted to remove the line that says PID=26416.... how could I do that, without writing the file over again? I can use external unix commands, however I am not very familiar with them so please if that is your suggestion, give an example. Thanks!

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Is there anyway to bring web @Context into JUnit (CXF+Spring)

- by Sudheer

I am trying to create unit test environment to test RESTFul services (cfx+spring) in my dev environemnt. To test RESTFul Services, I require @Context within JUnit test cases. @Context should contain HttpRequest, HttpSession, ServletContext, ServletConfig and all other webserver related information. I have setup the JUnit for the above, but when I run, @Context is coming as null. This could be because there is no webserver running and there is no @Context. I am just doubting whether there is a way to created sample web @Context and pass to JUnit. Any other ideas are welcome to bring web @Context into JUnit test cases. Thank you, Sudheer

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Pass Value between MDI Child in WinForm using C#

- by abhilashca

I have an MDI Parent, containing a MenuStrip. When I click on one of the Menu, two Child Forms are displayed simultaneoulsy. I have a TextBox and a Send Button on one of my ChildForm. When I type-in something in that TextBox and Click the Send Button, I need to show that value in the TextBox of my Second Child Form. What I had done is, I wrote a Public Function in the Second Child Form and tried to invoke it by creating an object of Second Form, on the Send Button click event. When I put break points, in that Public Function, I find that the control is flowing through that Public function on cliking the Send button. But the passed value is not displayed. And, I know that is not the standard way to do that. Any sample script for help? Thanks.

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