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  • What do you think is the best language for Bioinformatics?

    - by Ben Fossen
    I have done a couple research jobs in Bio-informatics and I have used Matlab for them. Matlab had a lot of powerful tools and was easy to use. I did thinks with genome sequencing and predicting metabolic pathways. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves best to Bio-informatics work that is math heavy and deals with a large amount of data.

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  • Regexp to extract sources from different video embeds

    - by Ben
    My SMF forum contains posts with video and I want to extract them to show on the Wordpress main page. My current regexp (thanks to SO!) extracts the url of the videos, which I embed using AutoEmbed. Everything works up until a post looks like this: <embed height="600" width="600" allowscriptaccess="never" quality="high" loop="true" play="true" src="http://mmavlog.net/embed/player.swf?file=http://video.ufc.tv/CSG/UFC113/20100507_ufc113_weigh_in_400k.flv" type="application/x-shockwave-flash"> Here is my current regexp: $regexp = "/\b(?:(?:https?|ftp):\/\/|www\.)[-a-z0-9+&@#\/%?=~_|!:,.;]*[-a-z0-9+&@#\/%=~_|]/i"; Since the posts can contain <embed> or <object> I realize that looking for the url by the "http" might be inaccurate. How can I use the regexp to look for "src=" for <embed> and "data=" for <object>?

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  • Default content editor in list form doesn't allow image alignment

    - by Ben Collins
    I need to be able to adjust the alignment of an image in an "Enhanced Rich Text Field" in an announcements list in MOSS 2007. However, the default content editor in the edit form for the list doesn't provide a way to do that. What's the fastest way for me to make sure users can align images? My first thought was to customize the DispForm.aspx and EditForm.aspx pages, but they just have the ListForm web part in the content region and as far as I know, you can't customize the ListForm web part from the designer.

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  • Undefined variable error when parsing json

    - by Ben Shelock
    I'm trying to parse the json grabbed from here. Basically what I do is iterate over the items, sort them, then display them. But I get an error saying data.data.children[i] is undefined. I can't think why it's doing it though? var json = 'http://www.reddit.com/reddits/mine/.json'; GM_xmlhttpRequest({ method: "GET", url: json, onload: reddits }); function reddits(response){ var txt = response.responseText; var data; var suggested = document.getElementById('suggested-reddits'); if(window.JSON && JSON.parse){ data = JSON.parse(txt); } else{ data = eval("("+txt+")"); } suggested.innerHTML += '<span>reddits you\'re subscribed to </span> <ul id="rsub"></ul>'; GM_addStyle('#rsub{width: 500px;}'); var reddits = new Array(); var rsub = document.getElementById('rsub'); for(i = 0; i <= data.data.children.length; i++){ var r = data.data.children[i].data.display_name; reddits.push(r); } sort(reddits); for(i = 0; i <= reddits.length; i++){ rsub.innerHTML += '<li><a href="#" onclick="set_sr_name(this); return false">' + reddits[i] + '</a></li>'; } }

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  • Mathematica equivalent of Ruby's inject

    - by Ben Alpert
    Is there a Mathematica function like inject in Ruby? For example, if I want the product of the elements in a list, in Ruby I can write: list.inject(1) { |prod,el| prod * el } I found I can just use Product in Mathematica: Apply[Product, list] However, this isn't general enough for me (like, if I don't just want the product or sum of the numbers). What's the closest equivalent to inject?

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  • The height and width properties on my Flex 4 app arn't working

    - by ben
    In the opening application tag of my Flex 4 app, I set the width and height properties as follows: <?xml version="1.0" encoding="utf-8"?> <s:Application xmlns:fx="http://ns.adobe.com/mxml/2009" xmlns:s="library://ns.adobe.com/flex/spark" xmlns:mx="library://ns.adobe.com/flex/mx" creationComplete="init()" backgroundColor.mainState="0x303030" xmlns:components="components.*" width="798" height="240"> What I go into Design mode in Flash Builder 4, the app is the correct size. But when I embed the .swf file into a HTML page, the application's background color covers the whole screen, and when the Flash Player Settings message box pops up it is outside of the area I defined in the code above. What am I doing wrong? Thanks for reading.

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  • Is READ UNCOMMITTED / NOLOCK safe in this situation?

    - by Ben Challenor
    I know that snapshot isolation would fix this problem, but I'm wondering if NOLOCK is safe in this specific case so that I can avoid the overhead. I have a table that looks something like this: drop table Data create table Data ( Id BIGINT NOT NULL, Date BIGINT NOT NULL, Value BIGINT, constraint Cx primary key (Date, Id) ) create nonclustered index Ix on Data (Id, Date) There are no updates to the table, ever. Deletes can occur but they should never contend with the SELECT because they affect the other, older end of the table. Inserts are regular and page splits to the (Id, Date) index are extremely common. I have a deadlock situation between a standard INSERT and a SELECT that looks like this: select top 1 Date, Value from Data where Id = @p0 order by Date desc because the INSERT acquires a lock on Cx (Date, Id; Value) and then Ix (Id, Date), but the SELECT acquires a lock on Ix (Id, Date) and then Cx (Date, Id; Value). This is because the SELECT first seeks on Ix and then joins to a seek on Cx. Swapping the clustered and non-clustered index would break this cycle, but it is not an acceptable solution because it would introduce cycles with other (more complex) SELECTs. If I add NOLOCK to the SELECT, can it go wrong in this case? Can it return: More than one row, even though I asked for TOP 1? No rows, even though one exists and has been committed? Worst of all, a row that doesn't satisfy the WHERE clause? I've done a lot of reading about this online, but the only reproductions of over- or under-count anomalies I've seen (one, two) involve a scan. This involves only seeks. Jeff Atwood has a post about using NOLOCK that generated a good discussion. I was particularly interested in a comment by Rick Townsend: Secondly, if you read dirty data, the risk you run is of reading the entirely wrong row. For example, if your select reads an index to find your row, then the update changes the location of the rows (e.g.: due to a page split or an update to the clustered index), when your select goes to read the actual data row, it's either no longer there, or a different row altogether! Is this possible with inserts only, and no updates? If so, then I guess even my seeks on an insert-only table could be dangerous. Update: I'm trying to figure out how snapshot isolation works. It seems to be row-based, where transactions read the table (with no shared lock!), find the row they are interested in, and then see if they need to get an old version of the row from the version store in tempdb. But in my case, no row will have more than one version, so the version store seems rather pointless. And if the row was found with no shared lock, how is it different to just using NOLOCK?

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  • SilverLight WebApp Calling Webservice in the same solution

    - by Ben
    Hi, I have a website solution that is composed of a SilverLight Project and an ASP Site that contains an asmx Webservice. The SilverLight project calls various methods in the Webservice, and this works fine on my home PC. When i publish the site (using 123-Reg if that makes a difference), it appears that the SilverLight app is no longer able to call the webservice. I have tried debugging the app by pointing my local version of the site to my published webservice and i get a "policy" issue. I know that 123 Reg have .Net 3.5 running on their servers, so i would assume that the site should "just work" when i publish it. Am i making a hugely stupid assumption there? Is there anything that i can do to change the "policies" within my app? Or is there another way around what i am trying to do ( i need to keep the webservice, as i want for it to be used from other places, and dont really want to duplicate code and create the same methods within the SilverLight project). Thanks

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  • In JSF - What is the correct way to do this? Two dropdown lists with dependency.

    - by Ben
    Hi, I'm making two dropdown lists in JSF which are dependent. Specifically, one list has all the languages and the second list contains values that are displayed in the currently selected language. I've implemented this by having the second list use information from a Hash and rebuilding that Hash in the setter of the currently selected language. JSF Code Bit: <rich:dropDownMenu value="#{bean.currentlySelectedLanguage}" id="languageSelector"> ... (binding to languages hash) ... <rich:dropDownMenu value="#{bean.currentlySelectedScript}" id="ScriptPullDown"> ... (binding to scripts hash) ... Backing Bean Code Bit: setCurrentlySelectedLanguage(String lang){ this.currentlySelectedLanguage = lang; rebuildScriptNames(lang); } I'm wondering if that's a good way of doing this or if theres a better method that I am not aware of. Thank you! EDIT - Adding info.. I used a a4j:support that with event="onchange" and ReRender="ScriptPullDown" to rerender the script pull down. I could probably add an action expression to run a method when the value changes. But is there a benefit to doing this over using code in the setter function?

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  • A hooked DirectX 9 program crashes on window resize, texture related.

    - by Ben
    I'm using EasyHook and SlimDX to overlay some graphics using SlimDX's Sprite and Texture classes. When I resize windows some programs fine, but others will crash - Winamp's MilkDrop 2 gives me an ambiguous memory error for example. I expect this is due to the after market Texture I created. The question is what VTable function should I hook and/or how/when do I dispose and recreate the Texture? Reset perhaps? If it isn't obvious I don't know much about DirectX.

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  • Android multiple screen sizes and density problems

    - by Ben Mc
    I'm having a real problem with my drawables that I just can't seem to figure out. The problem is this: There are screen sizes at approximately 320x480, 480x800, 480x854 Then there are most commonly densities at 1.0 (160) and 1.5 (240) Now, on a Droid, the screen size is 480x800 and the density is reporting using DisplayMetrics as 1.5 On the G1, it's 320x480 and reporting back at a density of 1.0 BUT tablet devices are reporting back at 480x800 with a density of 1.0 (160) So, I'm going mad because I can put 320x480 images in the drawables-mdpi folder and 480x800 images in the drawables-hdpi folder, but on Tablet computers, no matter what it's not resizing up anything to a full screen. Any help would be greatly appreciated. I just want all of my 320x480 images to scale up regardless of the device.

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  • iPhone: scroll view with arbitrary page/"settling" boundaries?

    - by Ben
    Hi all, I'm trying to figure out if I can get what I want out of UIScrollView through some trickery or whether I need to roll my own scroll view: I have a series of items in row that I want to scroll through. One item should always be centered in the view, but other items should be visible to either side. In other words, I want normal scrolling and edge bouncing, but I want the deceleration when the user ends a touch to naturally settle at some specified stop point. (Actually now that I think of it, this behavior is similar to coverflow in this respect.) I know UIScrollView doesn't do this out of the box, but does anyone have suggestions for how it might be made to do this, or if anyone's spotted any code that accomplishes something similar (I'm loathe to reimplement all the math for deceleration and edge bounce) Thanks!

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  • margin between content and div overflow scrollbar

    - by ben
    I am using the following bits of code to keep my menu items fixed while allowing for the scrolling of content because it seems to be the most stable method across all browsers. body { overflow: hidden; } div.content { height: 100%; overflow: auto; } My problem is simple, and yet I can not seem to figure it out, the content inside the tag butts up against the scrollbar for the div area and it makes reading much more difficult. How can I get a margin between them (apart from floating a transparent image to the right to create space, there HAS to be a better way)?

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  • LINQ Query using UDF that receives parameters from the query

    - by Ben Fidge
    I need help using a UDF in a LINQ which calculates a users position from a fixed point. int pointX = 567, int pointY = 534; // random points on a square grid var q = from n in _context.Users join m in _context.GetUserDistance(n.posY, n.posY, pointX, pointY, n.UserId) on n.UserId equals m.UserId select new User() { PosX = n.PosX, PosY = n.PosY, Distance = m.Distance, Name = n.Name, UserId = n.UserId }; The GetUserDistance is just a UDF that returns a single row in a TVP with that users distance from the points deisgnated in pointX and pointY variables, and the designer generates the following for it: [global::System.Data.Linq.Mapping.FunctionAttribute(Name="dbo.GetUserDistance", IsComposable=true)] public IQueryable<GetUserDistanceResult> GetUserDistance([global::System.Data.Linq.Mapping.ParameterAttribute(Name="X1", DbType="Int")] System.Nullable<int> x1, [global::System.Data.Linq.Mapping.ParameterAttribute(Name="X2", DbType="Int")] System.Nullable<int> x2, [global::System.Data.Linq.Mapping.ParameterAttribute(Name="Y1", DbType="Int")] System.Nullable<int> y1, [global::System.Data.Linq.Mapping.ParameterAttribute(Name="Y2", DbType="Int")] System.Nullable<int> y2, [global::System.Data.Linq.Mapping.ParameterAttribute(Name="UserId", DbType="Int")] System.Nullable<int> userId) { return this.CreateMethodCallQuery<GetUserDistanceResult>(this, ((MethodInfo)(MethodInfo.GetCurrentMethod())), x1, x2, y1, y2, userId); } when i try to compile i get The name 'n' does not exist in the current context

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  • License similar to the MIT license but without the ability to sell?

    - by Ben
    I'm trying to decide how I want to license my Wordpress themes to the public. I know that the GPL is recommended to Wordpress theme creators, however I feel it might not be liberal enough for me because I want businesses to be able to use them if they want to. I really like the MIT license, the only thing that gets me is the freedom to sell part. I don't want someone taking my themes and selling them on some theme farm site, they should be free for everyone, however I don't want to require them to republish any changes under the MIT as well, I think that that freedom should remain intact. Is there a license that sort of fits into the terms I specified here? I'm not a lawyer so I have trouble reading through the complicated language of licenses. If there is not a similar license to the MIT but with the terms I have specified, should I just license under a modified MIT? If so, can anyone help me write it? Thanks very much!

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  • C# webservice async callback not getting called on HTTP 407 error.

    - by Ben
    Hi, I am trying to test the use-case of a customer having a proxy with login credentials, trying to use our webservice from our client. If the request is synchronous, my job is easy. Catch the WebException, check for the 407 code, and prompt the user for the login credentials. However, for async requests, I seem to be running into a problem: the callback is never getting called! I ran a wireshark trace and did indeed see that the HTTP 407 error was being passed back, so I am bewildered as to what to do. Here is the code that sets up the callback and starts the request: TravelService.TravelServiceImplService svc = new TravelService.TravelServiceImplService(); svc.Url = svcUrl; svc.CreateEventCompleted += CbkCreateEventCompleted; svc.CreateEventAsync(crReq, req); And the code that was generated when I consumed the WSDL: public void CreateEventAsync(TravelServiceCreateEventRequest CreateEventRequest, object userState) { if ((this.CreateEventOperationCompleted == null)) { this.CreateEventOperationCompleted = new System.Threading.SendOrPostCallback(this.OnCreateEventOperationCompleted); } this.InvokeAsync("CreateEvent", new object[] { CreateEventRequest}, this.CreateEventOperationCompleted, userState); } private void OnCreateEventOperationCompleted(object arg) { if ((this.CreateEventCompleted != null)) { System.Web.Services.Protocols.InvokeCompletedEventArgs invokeArgs = ((System.Web.Services.Protocols.InvokeCompletedEventArgs)(arg)); this.CreateEventCompleted(this, new CreateEventCompletedEventArgs(invokeArgs.Results, invokeArgs.Error, invokeArgs.Cancelled, invokeArgs.UserState)); } } Debugging the WS code, I found that even the SoapHttpClientProtocol.InvokeAsync method was not calling its callback as well. Am I missing some sort of configuration?

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  • Consecutive 'if' statements

    - by Ben Packard
    How can I check one thing AND THEN another, if the first is true? For example, say I have a shopping basket object, and I only want to do something if the basket has been created AND it isn't empty. I've tried: if (basket && [basket numberOfItems >0])... But the second condition is evaluated even if the first fails, resulting in a crash (presumably because i'm calling numberOfItems on an object that doesn't exist). I can nest them, but this seems a bit ugly, and more to the point is problematic. Say I want to do one thing if the basket exists AND isn't empty, but another if either isn't true. That doesn't really work well in nested if statements.

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  • Meaning of Execute_priv on mysql.db table

    - by Ben Reisner
    I created user 'restriceduser' on my mysql server that is 'locked down'. The mysql.user table has a N for all priveledges for that account. The mysql.db table has Y for only Select, Insert, Update, Delete, Create, Drop; all other privileges are N for that account. I tried to create a stored procedure and then grant him access to run only that procedure, no others, but it does not work. The user receives: Error: execute command denied to user 'restricteduser'@'%' for routine 'mydb.functionname' The stored procedure: CREATE DEFINER = 'restriceduser'@'%' FUNCTION `functionname`(sIn MEDIUMTEXT, sformat MEDIUMTEXT) RETURNS int(11) NOT DETERMINISTIC CONTAINS SQL SQL SECURITY DEFINER COMMENT '' BEGIN .... END; The grant statement I tried: GRANT EXECUTE ON PROCEDURE mydb.functionname TO 'restricteduser'@'%'; I was able to work around by modifying his mysql.db entry with update mysql.db set execute_priv='Y' where user='restricteduser' This seems to be more then I want, because it opens up permissions for him to run any stored procedure in that database, while I only wanted him to have permissions to run the designated function. Does anyone see where my issue may lie?

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  • Scala and the Java Memory Model

    - by Ben Lings
    The Java Memory Model (since 1.5) treats final fields differently to non-final fields. In particular, provided the this reference doesn't escape during construction, writes to final fields in the constructor are guaranteed to be visible on other threads even if the object is made available to the other thread via a data race. (Writes to non-final fields aren't guaranteed to be visible, so if you improperly publish them, another thread could see them in a partially constructed state.) Is there any documentation on how/if the Scala compiler creates final (rather than non-final) backing fields for classes? I've looked through the language specification and searched the web but can't find any definitive answers. (In comparison the @scala.volatile annotation is documented to mark a field as volatile)

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  • (Not So) Silly Objective-C inheritance problem when using property - GCC Bug?

    - by Ben Packard
    Update 2 - Many people are insisting I need to declare an iVar for the property. Some are saying not so, as I am using Modern Runtime (64 bit). I can confirm that I have been successfully using @property without iVars for months now. Therefore, I think the 'correct' answer is an explanation as to why on 64bit I suddenly have to explicitly declare the iVar when (and only when) i'm going to access it from a child class. The only one I've seen so far is a possible GCC bug (thanks Yuji). Not so simple after all... Update - I messed up one line of the original copy and paste - corrected. The @property call was missing (nonatomic, retain) but is a red herring - STILL NEED AN ANSWER! Thanks. I've been scratching my head with this for a couple of hours - I haven't used inheritance much. Here I have set up a simple Test B class that inherits from Test A, where an ivar is declared. But I get the compilation error that the variable is undeclared. This only happens when I add the property and synthesize declarations - works fine without them. TestA Header: #import <Cocoa/Cocoa.h> @interface TestA : NSObject { NSString *testString; } @end TestA Implementation is empty: #import "TestA.h" @implementation TestA @end TestB Header: #import <Cocoa/Cocoa.h> #import "TestA.h" @interface TestB : TestA { } @property (nonatomic, retain) NSString *testProp; @end TestB Implementation (Error - 'testString' is undeclared) #import "TestB.h" @implementation TestB @synthesize testProp; - (void)testing{ NSLog(@"test ivar is %@", testString); } @end

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  • Avoiding secondary selects or joins with Hibernate Criteria or HQL query

    - by Ben Benson
    I am having trouble optimizing Hibernate queries to avoid performing joins or secondary selects. When a Hibernate query is performed (criteria or hql), such as the following: return getSession().createQuery(("from GiftCard as card where card.recipientNotificationRequested=1").list(); ... and the where clause examines properties that do not require any joins with other tables... but Hibernate still performs a full join with other tables (or secondary selects depending on how I set the fetchMode). The object in question (GiftCard) has a couple ManyToOne associations that I would prefer to be lazily loaded in this case (but not necessarily all cases). I want a solution that I can control what is lazily loaded when I perform the query. Here's what the GiftCard Entity looks like: @Entity @Table(name = "giftCards") public class GiftCard implements Serializable { private static final long serialVersionUID = 1L; private String id_; private User buyer_; private boolean isRecipientNotificationRequested_; @Id public String getId() { return this.id_; } public void setId(String id) { this.id_ = id; } @ManyToOne @JoinColumn(name = "buyerUserId") @NotFound(action = NotFoundAction.IGNORE) public User getBuyer() { return this.buyer_; } public void setBuyer(User buyer) { this.buyer_ = buyer; } @Column(name="isRecipientNotificationRequested", nullable=false, columnDefinition="tinyint") public boolean isRecipientNotificationRequested() { return this.isRecipientNotificationRequested_; } public void setRecipientNotificationRequested(boolean isRecipientNotificationRequested) { this.isRecipientNotificationRequested_ = isRecipientNotificationRequested; } }

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