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  • 50 sequences in one line

    - by user343934
    I have alignment file and long record in it. Suppose while displaying to an end user i want to show Sequence ID and 50 sequences in each line and continue further till the end of file. Can anyone suggest me algorithm or example code in python. Thanks in advance

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  • POSIX: allocate 64KB on 64KB boundary.

    - by Eloff
    I would really like to actually only allocate 64KB of memory, not 128KB and then do the alignment manually - far too wasteful. VirtualAlloc on windows gives precisely this behavior. Supposedly there's code in SquirrelFish for doing this on just about every platform, but I haven't managed to locate it. Is there a space efficient way to allocate 64KB on a 64KB boundary in POSIX? Failing that, in Linux?

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  • Can anyone tell me why these lines are not working?

    - by user343934
    I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess from Bio import AlignIO from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input="c:\Python26\opuntia.fasta") child= subprocess.Popen(str(cline), stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) align=AlignIO.read(child.stdout,"fasta") outfile=open('c:\Python26\opuntia.phy','w') AlignIO.write([align],outfile,'phylip') outfile.close() I always encounter with these problems Traceback (most recent call last): File "", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in align=AlignIO.read(child.stdout,"fasta") File "C:\Python26\Lib\site-packages\Bio\AlignIO_init_.py", line 423, in read raise ValueError("No records found in handle") ValueError: No records found in handle

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  • jframe adding own design jinternal frame error

    - by Van Minh
    I designed a title bar color on my JInternal frame. Then I took attempt to add it to my JFrame, but I cannot. Here is the code of my title bar: public class MyIFtitleBar extends BasicInternalFrameTitlePane { public MyIFtitleBar(JInternalFrame jif) { super(jif); } protected void paintTitleBackground(Graphics g){ g.setColor(Color.pink); g.fillRect(0, 0, getWidth(), getHeight()); } } Here is my JInternal frame. I tried running it in its psvm method, that worked! public class FitnessProg_Frame extends javax.swing.JInternalFrame { public FitnessProg_Frame() { initComponents(); this.setUI(new BasicInternalFrameUI(this){ @Override protected JComponent createNorthPane(JInternalFrame jif) { return new MyIFtitleBar(jif); } }); } @SuppressWarnings("unchecked") private void initComponents() { setBackground(new java.awt.Color(255, 255, 255)); setBorder(new javax.swing.border.MatteBorder(null)); setTitle("Fitness Progarm"); setPreferredSize(new java.awt.Dimension(507, 304)); pack(); } } But when I add it to my JFrame I get an error: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException Here is my JFrame code: public class NewJFrame extends javax.swing.JFrame { public NewJFrame() { initComponents(); FitnessProg_Frame ff = new FitnessProg_Frame(); ff.setVisible(true); mydes.add(ff); // this line made errors } @SuppressWarnings("unchecked") private void initComponents() { mydes = new javax.swing.JDesktopPane(); setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE); javax.swing.GroupLayout mydesLayout = new javax.swing.GroupLayout(mydes); mydes.setLayout(mydesLayout); mydesLayout.setHorizontalGroup( mydesLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGap(0, 400, Short.MAX_VALUE) ); mydesLayout.setVerticalGroup( mydesLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGap(0, 300, Short.MAX_VALUE) ); getContentPane().add(mydes, java.awt.BorderLayout.CENTER); pack(); } public static void main(String args[]) { try { for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) { if ("Nimbus".equals(info.getName())) { javax.swing.UIManager.setLookAndFeel(info.getClassName()); break; } } } catch (ClassNotFoundException ex) { java.util.logging.Logger.getLogger(NewJFrame.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } catch (InstantiationException ex) { java.util.logging.Logger.getLogger(NewJFrame.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } catch (IllegalAccessException ex) { java.util.logging.Logger.getLogger(NewJFrame.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } catch (javax.swing.UnsupportedLookAndFeelException ex) { java.util.logging.Logger.getLogger(NewJFrame.class.getName()).log(java.util.logging.Level.SEVERE, null, ex); } java.awt.EventQueue.invokeLater(new Runnable() { public void run() { new NewJFrame().setVisible(true); } }); } private javax.swing.JDesktopPane mydes; }

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  • Display Malformed HTML "Safely?"

    - by yar
    Let's say I have some HTML like this: <ol><li>a knock at the door, I'll be back in a second which I display as inline HTML within a div that I produce. Is there any way to stop the inner, malformed HTML from screwing up the alignment of the entire document that comes after the HTML? I realize that intelligently parsing it is one option (since I do have it on the server side), but I'm looking for a lighter solution.

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  • CSS check for Chrome, IE, Firefox

    - by hankh
    I've noticed a small alignment issue in the three major browsers when rendering my web site. As such how can I perform the following pseudo-code with pure CSS? if Webkit (Safari/Chrome) { #myDIV {margin-top:-3px} } else if (Firefox) { #myDIV {margin-top:0px} } else { // IE and other browsers #myDIV {margin-top:1px} }

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  • Showing calendar Control...

    - by Brigadier Jigar
    Hi all... I am creating a web application in which i have to select a date. I am using Calendar control. But it occupies too much space and other labels and text boxes are not shown in proper alignment. Is there anything I Can do in which when i click on an image, the calendar control opens, but on the textbox, so that it does not occupy any space. Regards, Jigar

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  • Parsing line with delimiter in Python

    - by neversaint
    I have lines of data which I want to parse. The data looks like this: a score=216 expect=1.05e-06 a score=180 expect=0.0394 What I want to do is to have a subroutine that parse them and return 2 values (score and expect) for each line. However this function of mine doesn't seem to work: def scoreEvalFromMaf(mafLines): for word in mafLines[0]: if word.startswith("score="): theScore = word.split('=')[1] theEval = word.split('=')[2] return [theScore, theEval] raise Exception("encountered an alignment without a score") Please advice what's the right way to do it?

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  • A column of a table needs to stay in one line (HTML/CSS/Javascript)

    - by Julien
    Hi Folks ! So I am having an issue on my entrepreneur business opportunity rating matrix : I would like the radio buttons to stay on the same line. The problem is that I don't know how I should process because if I give a fixed minimum width for the cell, i'm not sure it will display properly on other browsers, and if the cell is to big I loose the alignment of the radio buttons. Do you guys have a CSS/Javascript (jQuery) trick that would fix this ? Thank you

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  • How can I pick multiple images from the built-in picker Intent?

    - by dguardi
    Is it possible to reuse the picker Intent to select multiple pictures instead of one? I haven't found a way and I'm trying to reproduce it with a grid view but my alignment is very poor and my performance is not quite as good as the picker. Intent photoPickerIntent = new Intent(Intent.ACTION_PICK); photoPickerIntent.setType("image/*"); startActivityForResult(photoPickerIntent, REQ_PICKER);

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  • How to align a UITableView's text?

    - by Knodel
    In my app I have a UITableView and I want to change the text's alignment to center (not only from the sides like this cell.textAlignment = UITextAlignmentCenter; but from up and down, as well). Can you help me? thanks in advance!

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  • How to find padding space around the label text?

    - by Ganesh
    I am adding a label controls at run time. I can add or modify text in label and can change the font also.Now my problem is When i changed the font of text in label, alignment is not proper,its due to padding.Is there any way to find how much padding is ocured [ed: obscured?] based on font?

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  • Lifting a math symbol in LaTeX

    - by Chris Conway
    I'm using the symbol \otimes as a unary operator and it's vertical alignment doesn't seem right to me. It wants to sit a bit below the baseline: and I tried using \raisebox to fix this, e.g., \raisebox{1pt}{$\otimes$}: But \raisebox doesn't seem to be sensitive to subscripts. The operator stays the same size while everything around it shrinks: The problem, I think, is that \raisebox creates its own LR box, which doesn't inherit the settings in the surrounding math environment. Is there a version of \raisebox that "respects math"?

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  • Sphere entering in to the cube.unity

    - by Parthi
    I am trying Roll a Ball unity tutorial.Everything is fine,but when I roll the ball it is moving through the cube instead of picking it. my player class is using UnityEngine; using System.Collections; public class player : MonoBehaviour { public float speed; // Use this for initialization // Update is called once per frame void Update () { float h = Input.GetAxis("Horizontal"); float v = Input.GetAxis("Vertical"); Vector3 move = new Vector3(h,0,v); rigidbody.AddForce(move * speed * Time.deltaTime); } void OnTriggerEnter(Collider other) { if(other.gameObject.tag == "Pick up") { other.gameObject.SetActive(false); } } }

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  • Graphical Error During Installation of Ubuntu 13.10 32bit

    - by user172353
    In trying to install the latest version of Ubuntu, I made a bootable USB and proceeded to give it a shot. As it loaded, the upper half of the screen displayed staticy, multi-colored horizontal lines, but continued to boot into the installer. The installer appeared to be functional using the keyboard, but I was unable to proceed as the graphical display was a mismatched mosaic of the proper screen with no visible cursor. I'll try to edit in a photo later. Attempting the exact same USB on a different device (an old Asus Eee 1005HA) gave no such error and installed without a hitch.

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  • Goodbye XML&hellip; Hello YAML (part 2)

    - by Brian Genisio's House Of Bilz
    Part 1 After I explained my motivation for using YAML instead of XML for my data, I got a lot of people asking me what type of tooling is available in the .Net space for consuming YAML.  In this post, I will discuss a nice tooling option as well as describe some small modifications to leverage the extremely powerful dynamic capabilities of C# 4.0.  I will be referring to the following YAML file throughout this post Recipe: Title: Macaroni and Cheese Description: My favorite comfort food. Author: Brian Genisio TimeToPrepare: 30 Minutes Ingredients: - Name: Cheese Quantity: 3 Units: cups - Name: Macaroni Quantity: 16 Units: oz Steps: - Number: 1 Description: Cook the macaroni - Number: 2 Description: Melt the cheese - Number: 3 Description: Mix the cooked macaroni with the melted cheese Tooling It turns out that there are several implementations of YAML tools out there.  The neatest one, in my opinion, is YAML for .NET, Visual Studio and Powershell.  It includes a great editor plug-in for Visual Studio as well as YamlCore, which is a parsing engine for .Net.  It is in active development still, but it is certainly enough to get you going with YAML in .Net.  Start by referenceing YamlCore.dll, load your document, and you are on your way.  Here is an example of using the parser to get the title of the Recipe: var yaml = YamlLanguage.FileTo("Data.yaml") as Hashtable; var recipe = yaml["Recipe"] as Hashtable; var title = recipe["Title"] as string; In a similar way, you can access data in the Ingredients set: var yaml = YamlLanguage.FileTo("Data.yaml") as Hashtable; var recipe = yaml["Recipe"] as Hashtable; var ingredients = recipe["Ingredients"] as ArrayList; foreach (Hashtable ingredient in ingredients) { var name = ingredient["Name"] as string; } You may have noticed that YamlCore uses non-generic Hashtables and ArrayLists.  This is because YamlCore was designed to work in all .Net versions, including 1.0.  Everything in the parsed tree is one of two things: Hashtable, ArrayList or Value type (usually String).  This translates well to the YAML structure where everything is either a Map, a Set or a Value.  Taking it further Personally, I really dislike writing code like this.  Years ago, I promised myself to never write the words Hashtable or ArrayList in my .Net code again.  They are ugly, mostly depreciated collections that existed before we got generics in C# 2.0.  Now, especially that we have dynamic capabilities in C# 4.0, we can do a lot better than this.  With a relatively small amount of code, you can wrap the Hashtables and Array lists with a dynamic wrapper (wrapper code at the bottom of this post).  The same code can be re-written to look like this: dynamic doc = YamlDoc.Load("Data.yaml"); var title = doc.Recipe.Title; And dynamic doc = YamlDoc.Load("Data.yaml"); foreach (dynamic ingredient in doc.Recipe.Ingredients) { var name = ingredient.Name; } I significantly prefer this code over the previous.  That’s not all… the magic really happens when we take this concept into WPF.  With a single line of code, you can bind to the data dynamically in the view: DataContext = YamlDoc.Load("Data.yaml"); Then, your XAML is extremely straight-forward (Nothing else.  No static types, no adapter code.  Nothing): <StackPanel> <TextBlock Text="{Binding Recipe.Title}" /> <TextBlock Text="{Binding Recipe.Description}" /> <TextBlock Text="{Binding Recipe.Author}" /> <TextBlock Text="{Binding Recipe.TimeToPrepare}" /> <TextBlock Text="Ingredients:" FontWeight="Bold" /> <ItemsControl ItemsSource="{Binding Recipe.Ingredients}" Margin="10,0,0,0"> <ItemsControl.ItemTemplate> <DataTemplate> <StackPanel Orientation="Horizontal"> <TextBlock Text="{Binding Quantity}" /> <TextBlock Text=" " /> <TextBlock Text="{Binding Units}" /> <TextBlock Text=" of " /> <TextBlock Text="{Binding Name}" /> </StackPanel> </DataTemplate> </ItemsControl.ItemTemplate> </ItemsControl> <TextBlock Text="Steps:" FontWeight="Bold" /> <ItemsControl ItemsSource="{Binding Recipe.Steps}" Margin="10,0,0,0"> <ItemsControl.ItemTemplate> <DataTemplate> <StackPanel Orientation="Horizontal"> <TextBlock Text="{Binding Number}" /> <TextBlock Text=": " /> <TextBlock Text="{Binding Description}" /> </StackPanel> </DataTemplate> </ItemsControl.ItemTemplate> </ItemsControl> </StackPanel> This nifty XAML binding trick only works in WPF, unfortunately.  Silverlight handles binding differently, so they don’t support binding to dynamic objects as of late (March 2010).  This, in my opinion, is a major lacking feature in Silverlight and I really hope we will see this feature available to us in Silverlight 4 Release.  (I am not very optimistic for Silverlight 4, but I can hope for the feature in Silverlight 5, can’t I?) Conclusion I still have a few things I want to say about using YAML in the .Net space including de-serialization and using IronRuby for your YAML parser, but this post is hopefully enough to see how easy it is to incorporate YAML documents in your code. Codeplex Site for YAML tools Dynamic wrapper for YamlCore

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  • How can I reorient the axes of an object?

    - by d3vid
    I spent some time in Unity yesterday trying to fire a sphere from a horizontal cylinder (like a ball from a cannon). I was using Vector3.forward, but the sphere kept coming out the top of the cylinder rather than the front. Someone suggested using Vector3.up instead, and sure enough it worked! The cylinder is vertical by default. So, it appears that when I rotated the cylinder by 90 degrees to lay it flat, the local axes remained the same. The relative front of the cylinder remained at the same point, so when I fired the sphere it shot out the new "top", not what looked to me like the "front". If I had happened to be facing the other way, I would have had to fire at Vector3.down instead. How can I reorient/reset the axes of an object so that they match my expectations? (And if I can't, how can I tell by looking which way an object is oriented?)

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  • Surface and the Uphill Battle to Win Over iPad Users (Namely: Me)

    - by D'Arcy Lussier
    I went away this past weekend and decided to bring along the Windows 8 tablet from the Build conference last year – y’know, to give Windows 8 a try in a typical scenario. I also brought our iPad 2 along since I figured my wife would want to use that. I’d love to tell you how I found using my Windows 8 tablet but I can’t – I used the iPad exclusively the entire weekend. It was during this that I realized what Microsoft needs to do to win me over as an iPad user. As you’ll see, I’m left wondering what it is that Surface is meant to compete with: iPad and other tablets, or thin laptops like the MacBook Air or Ultrabooks. Device Size I really like the size of the iPad compared with the Build tablet. It’s not as long and the thinness/weight of the device makes it feel more like you’re holding a magazine than a computer. I’m pleased that Microsoft will be matching the thinness of the iPad with Surface, but I’m suspect as to what that actually means. The iPad’s edges slant inwards where the Surface has a thicker boxish look (similar to the iPhone 4S). So while they may have the same depth at the deepest part of both devices, I bet the iPad will come off feeling thinner. However, its not lost on me the number of external port options the Surface’s design provides over the iPad (Usb, etc.). With that said, I haven’t missed having a USB slot on my iPad. I’m not a fan of lengthening the Surface screen size to almost a full inch over the iPad, mainly because… Vertical Orientation Experience Did you notice at the announce event, in the images of the devices that have been released, and in any marketing for it, that the surface is always displayed in horizontal orientation. This is a huge beef I have with my Build tablet and why I prefer the iPad. Yes the iPad can do the wide-screenish mode, but the iPad is oriented to be vertical by nature. Don’t agree? Look at the button and camera placement – both on the shorter sides of the device. Compare that with the Surface, where the orientation for the button and camera is on the longer sides. To be fair, Blackberry and the horde of Android tablets out there haven’t gotten this either – since most monitors are widescreen nowadays tablets should be too right? Wrong. Widescreen is great for certain things, but tasks such as reading is not one of them – hence why monitor companies like Dell provide stands that allow you to flip your widescreen monitor to a vertical orientation. That Microsoft has chosen a horizontal orientation by default for Windows 8 is disappointing – hopefully hardware manufacturers will be given the option of a default vertical orientation. Fast Startup Time I like that I can turn off/turn on the iPad very quickly. Even from a true “off” mode and not just sleeping, the iPad boots up very quickly. Windows RT needs to have that same quick response. If I start finding that I’m waiting for the device to boot up for more than 30 seconds that could be a show stopper. No Heat I really hate that the Build tablet has fans that kick in to cool the procs, but its basically a slate computer and I get its part of that prototype build. For Surface, it needs to be the same type of experience as the iPad – no heat! I know Surface doesn’t have fans and uses some cool new vent system or something like that, but even then – I want to sit and read a book on my Surface without having to feel any heat coming from the device, which is the experience I have with the iPad now. What About Apps?! I am definitely not the target client when it comes to app stores. On my iPad I use: Safari Kindle Reader Twitter App Settlers of Catan TSN’s App And that’s it. So really, while its nice that some version of Office might be available, I’m not planning on utilizing a Surface for creating a PowerPoint or working on a Word document – that’s what my laptop is for. I want my tablet to be for information snacking or as an e-reader and occasionally an entertainment device. Surface vs iPad or Surface vs Air? The more that I read up on Surface, the more I wonder if it won’t be a touch-enabled MacBook Air competitor more than an iPad one. Also, I really question if Microsoft gets tablets – when one of your main selling features is a built-in physical keyboard it speaks more to a traditional laptop experience than a tablet one that’s entirely reliant on touch. Still, I really love the Windows Phone interface – way more than iOS – so I’m still very optimistic that the Metro experience on the tablet will be fantastic. I just worry that Microsoft has interpreted a tablet as a computer with a removable keyboard and a touch screen, and that’s not what tablet computing is about at all.

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  • Visual Studio Little Wonders: Box Selection

    - by James Michael Hare
    So this week I decided I’d do a Little Wonder of a different kind and focus on an underused IDE improvement: Visual Studio’s Box Selection capability. This is a handy feature that many people still don’t realize was made available in Visual Studio 2010 (and beyond).  True, there have been other editors in the past with this capability, but now that it’s fully part of Visual Studio we can enjoy it’s goodness from within our own IDE. So, for those of you who don’t know what box selection is and what it allows you to do, read on! Sometimes, we want to select beyond the horizontal… The problem with traditional text selection in many editors is that it is horizontally oriented.  Sure, you can select multiple rows, but if you do you will pull in the entire row (at least for the middle rows).  Under the old selection scheme, if you wanted to select a portion of text from each row (a “box” of text) you were out of luck.  Box selection rectifies this by allowing you to select a box of text that bounded by a selection rectangle that you can grow horizontally or vertically.  So let’s think a situation that could occur where this comes in handy. Let’s say, for instance, that we are defining an enum in our code that we want to be able to translate into some string values (possibly to be stored in a database, output to screen, etc.). Perhaps such an enum would look like this: 1: public enum OrderType 2: { 3: Buy, // buy shares of a commodity 4: Sell, // sell shares of a commodity 5: Exchange, // exchange one commodity for another 6: Cancel, // cancel an order for a commodity 7: } 8:  Now, let’s say we are in the process of creating a Dictionary<K,V> to translate our OrderType: 1: var translator = new Dictionary<OrderType, string> 2: { 3: // do I really want to retype all this??? 4: }; Yes the example above is contrived so that we will pull some garbage if we do a multi-line select. I could select the lines above using the traditional multi-line selection: And then paste them into the translator code, which would result in this: 1: var translator = new Dictionary<OrderType, string> 2: { 3: Buy, // buy shares of a commodity 4: Sell, // sell shares of a commodity 5: Exchange, // exchange one commodity for another 6: Cancel, // cancel an order for a commodity 7: }; But I have a lot of junk there, sure I can manually clear it out, or use some search and replace magic, but if this were hundreds of lines instead of just a few that would quickly become cumbersome. The Box Selection Now that we have the ability to create box selections, we can select the box of text to delete!  Most of us are familiar with the fact we can drag the mouse (or hold [Shift] and use the arrow keys) to create a selection that can span multiple rows: Box selection, however, actually allows us to select a box instead of the typical horizontal lines: Then we can press the [delete] key and the pesky comments are all gone! You can do this either by holding down [Alt] while you select with your mouse, or by holding down [Alt+Shift] and using the arrow keys on the keyboard to grow the box horizontally or vertically. So now we have: 1: var translator = new Dictionary<OrderType, string> 2: { 3: Buy, 4: Sell, 5: Exchange, 6: Cancel, 7: }; Which is closer, but we still need an opening curly, the string to translate to, and the closing curly and comma. Fortunately, again, this is easy with box selections due to the fact box selection can even work for a zero-width selection! That is, hold down [Alt] and either drag down with no width, or hold down [Alt+Shift] and arrow down and you will define a selection range with no width, essentially, a vertical line selection: Notice the faint selection line on the right? So why is this useful? Well, just like with any selected range, we can type and it will replace the selection. What does this mean for box selections? It means that we can insert the same text all the way down on each line! If we have the same selection above, and type a curly and a space, we’d get: Imagine doing this over hundreds of lines and think of what a time saver it could be! Now make a zero-width selection on the other side: And type a curly and a comma, and we’d get: So close! Now finally, imagine we’ve already defined these strings somewhere and want to paste them in: 1: const private string BuyText = "Buy Shares"; 2: const private string SellText = "Sell Shares"; 3: const private string ExchangeText = "Exchange"; 4: const private string CancelText = "Cancel"; We can, again, use our box selection to pull out the constant names: And clicking copy (or [CTRL+C]) and then selecting a range to paste into: And finally clicking paste (or [CTRL+V]) to get the final result: 1: var translator = new Dictionary<OrderType, string> 2: { 3: { Buy, BuyText }, 4: { Sell, SellText }, 5: { Exchange, ExchangeText }, 6: { Cancel, CancelText }, 7: };   Sure, this was a contrived example, but I’m sure you’ll agree that it adds myriad possibilities of new ways to copy and paste vertical selections, as well as inserting text across a vertical slice. Summary: While box selection has been around in other editors, we finally get to experience it in VS2010 and beyond. It is extremely handy for selecting columns of information for cutting, copying, and pasting. In addition, it allows you to create a zero-width vertical insertion point that can be used to enter the same text across multiple rows. Imagine the time you can save adding repetitive code across multiple lines!  Try it, the more you use it, the more you’ll love it! Technorati Tags: C#,CSharp,.NET,Visual Studio,Little Wonders,Box Selection

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  • Level selection view - similiar to Angry Bird's

    - by Piotr
    I am making game and need to prepare view for level selection. Could you recommend me some opensource library which could I use? I need icons to vibrate after long pressing one of them, some callbacks after choosing them, possibility to prepare custom icon's view, page control and horizontal scrolling. I was trying to use OpenSpringBoard but weirdly couldn't see scrollview and pagecontrol working in this project - it seems that there's possibility to use only one page. On the other hand, myLauncher(https://github.com/dlinsin/myLauncher) isn't so easy to include in project, as I need a seperate view with some delegate methods. I need to be compatible with iOS 4.2

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