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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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• Struts2 dynamic form elements

  - by bozo

  Hi, I would like to create little higer-level framework on top of Stuts2 which can take form element description from Action and render a complete form, in order to avoid having a separate JSP files with hardcoded form elements for every form in a large web application (so if I manage to do this I will have just a few generic JSPs for data form and few for layout). Application is extremely data-driven. My idea is to create form description using custom objects in the Action (i.e. Button, TextInput etc.) and then to create a single JSP page that will render eveything out. What is the best way of doing this? Can you propose some concrete way to do this? I don't want to write something if I can reuse the existing code with some effort. Any ideas are appreciated. Kind regards, Bozo

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• Hudson interactive mode:- Is there one?

  - by Rupal Desai

  I'm pretty new to hudson build system. I currently have my builds run from combination of perl/cgi scripts, with ability to start from a browser. What I need is an ability in hudson to checkout a file from perforce (can do that), parse that file (i can write a script for this) and based on the result of the parse give the user ability to choose various different options on what to build (compile). Is this possible? I'm not sure if I should tie together couple of different projects to do this or not? Any ideas on this could be achieved would be very helpful.

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• Scrapy Could not find spider Error

  - by Nacari

  I have been trying to get a simple spider to run with scrapy, but keep getting the error: Could not find spider for domain:stackexchange.com when I run the code with the expression scrapy-ctl.py crawl stackexchange.com. The spider is as follow: from scrapy.spider import BaseSpider from __future__ import absolute_import class StackExchangeSpider(BaseSpider): domain_name = "stackexchange.com" start_urls = [ "http://www.stackexchange.com/", ] def parse(self, response): filename = response.url.split("/")[-2] open(filename, 'wb').write(response.body) SPIDER = StackExchangeSpider()` Another person posted almost the exact same problem months ago but did not say how they fixed it, http://stackoverflow.com/questions/1806990/scrapy-spider-is-not-working I have been following the turtorial exactly at http://doc.scrapy.org/intro/tutorial.html, and cannot figure out why it is not working.

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• Writing Facebook apps in C#

  - by Water Cooler v2

  Hi, I am a C# developer and fancy the idea of writing a C# app or two to integrate with the Facebook API. I read from this page: http://wiki.developers.facebook.com/index.php/User:C_Sharp that there's this Microsoft SDK for Facebook Platform that has binary assemblies that I can use to write my C# app. As a start, I want to try out the example mentioned on the above-mentioned page -- one that gets me a friend list. The problem is: I am completely new to this Facebook development thing and I see I am going to need, at the very least, an API Key and some Facebook service Secret key or some such, to begin writing some code. Do I also need a developer account? Where do I get all these things from?

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• Using PIG with Hadoop, how do I regex match parts of text with an unknown number of groups?

  - by lmonson

  I'm using Amazon's elastic map reduce. I have log files that look something like this random text foo="1" more random text foo="2" more text noise foo="1" blah blah blah foo="1" blah blah foo="3" blah blah foo="4" ... How can I write a pig expression to pick out all the numbers in the 'foo' expressions? I prefer tuples that look something like this: (1,2) (1) (1,3,4) I've tried the following: TUPLES = foreach LINES generate FLATTEN(EXTRACT(line,'foo="([0-9]+)"')); But this yields only the first match in each line: (1) (1) (1)

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• What's so bad about in-line CSS?

  - by ChessWhiz

  When I see website starter code and examples, the CSS is always in a separate file, named something like "main.css", "default.css", or "Site.css". However, when I'm coding up a page, I'm often tempted to throw the CSS in-line with a DOM element, such as by setting "float: right" on an image. I get the feeling that this is "bad coding", since it's so rarely done in examples. I understand that if the style will be applied to multiple objects, it's wise to follow "Don't Repeat Yourself" (DRY) and assign it to a CSS class to be referenced by each element. However, if I won't be repeating the CSS on another element, why not in-line the CSS as I write the HTML? The question: Is using in-line CSS considered bad, even if it will only be used on that element? If so, why? Example (is this bad?): <img src="myimage.gif" style="float:right" />

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• Ajax data two-way data binding strategies?

  - by morgancodes

  I'd like to 1) Draw create form fields and populate them with data from javascript objects 2) Update those backing objects whenever the value of the form field changes Number 1 is easy. I have a few js template systems I've been using that work quite nicely. Number 2 may require a bit of thought. A quick google search on "ajax data binding" turned up a few systems which seem basically one-way. They're designed to update a UI based on backing js objects, but don't seem to address the question of how to update those backing objects when changes are made to the UI. Can anyone recommend any libraries which will do this for me? It's something I can write myself without too much trouble, but if this question has already been thought through, I'd rather not duplicate the work.

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• Import Namespace System.Query

  - by GateKiller

  I am trying to load Linq on my .Net 3.5 enabled web server by adding the following to my .aspx page: <%@ Import Namespace="System.Query" %> However, this fails and tells me it cannot find the namespace. The type or namespace name 'Query' does not exist in the namespace 'System' I have also tried with no luck: System.Data.Linq System.Linq System.Xml.Linq I believe that .Net 3.5 is working because var hello = "Hello World" seems to work. Can anyone help please? Cheers, Stephen PS: I just want to clarify that I don't use Visual Studio, I simple have a Text Editor and write my code directly into .aspx files.

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• Is there a production ready web application framework in Python?

  - by peperg

  I heard lots of good opinions about Python language. They say it's mature, expressive etc... Are there any production-ready web application frameworks in Python. By "production ready" I mean : supports objective-relational mapping with caching and declarative desciption (like JPA, Hibernate etc..) controls oriented user interface support - no HTML templates but something like JSF (RichFaces, Icefaces) or GWT, Vaadin, ZK component decomposition and dependency injection (like EJB or Spring) unit and integration testing good IDE support clustering, modularity etc (like Terracota, OSGi etc..) there are successful applications written in it by companies like IBM, Oracle etc (I mean real business applications not Twitter) could have commercial support Is it possible at all in Python world ? Or only choices are : use Python and write everything from the bottom (too expensice) stick to JEE buy .NET stack

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• VBA Excel To SqlServer

  - by adrianm

  What is the best way to write VBA code to connect to SQL Server 2005 from Excel? The users of the excel file might run XP, Vista, Win7 and I want to prevent driver installation as much as possible. My understanding is that XP uses MDAC while Vista/Win7 uses DAC. Does that mean that a reference to MDAC 2.8 will not work on a Vista machine and the other way around? Will my VBA code work on both if I don't add a reference and use late binding, e.g. CreateObject("ADODB.Connection")?

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• Chipmunk warning still present with --release

  - by Kaliber64

  I'm using Python27 on Windows 7 64-bit. I downloaded the source for Chipmunk 6.2.x and compiled Pymunk with --release and -c ming32. Almost zero problems. Lots of path not found cause I'm bad. All prints seem to have disappeared but I get spammed with EPA iteration warnings. I've seen a couple discussions but no solutions. Possible chipmunk betas to fix the float errors causing the double truths causing the warning. I picked the latest stable version I think. My program is seriously bogged down with all the prints. class NullDevice(): def write(self, s): pass sys.stdout=NullDevice() Does not disable the C prints .< Any help?

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• VB.NET overloading array access?

  - by Wayne Werner

  Hi, Is it possible to overload the array/dict access operators in VB.net? For example, you can state something like: Dim mydict As New Hashtable() mydict.add("Cool guy", "Overloading is dangerous!") mydict("Cool guy") = "Overloading is cool!" And that works just fine. But what I would like to do is be able to say: mydict("Cool guy") = "3" and then have 3 automagically converted to the Integer 3. I mean, sure I can have a private member mydict.coolguy and have setCoolguy() and getCoolguy() methods, but I would prefer to be able to write it the former way if at all possible. Thanks

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• How to get all paths in drupal install

  - by Aaron

  Hi, I need to write a module that gives me a page will all possible paths in a drupal install, including orphaned pages. (site map won't work for that). I can query the url_alias table for aliases, and I can query the menu_router table for all paths, even ones set in page/feed displays in views. But, variable paths (those with arguments) get interpreted at run-time. So, is there a way to get all possible paths in a drupal install, including dynamic paths and orphans? It's catch22. I have to know all the urls ahead of time to get them.

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• Android serialization: ImageView

  - by embo

  I have a simple class: public class Ball2 extends ImageView implements Serializable { public Ball2(Context context) { super(context); } } Serialization ok: private void saveState() throws IOException { ObjectOutputStream oos = new ObjectOutputStream(openFileOutput("data", MODE_PRIVATE)); try { Ball2 data = new Ball2(Game2.this); oos.writeObject(data); oos.flush(); } catch (Exception e) { Log.e("write error", e.getMessage(), e); } finally { oos.close(); } } But deserealization private void loadState() throws IOException { ObjectInputStream ois = new ObjectInputStream(openFileInput("data")); try { Ball2 data = (Ball2) ois.readObject(); } catch (Exception e) { Log.e("read error", e.getMessage(), e); } finally { ois.close(); } } fail with error: 03-24 21:52:43.305: ERROR/read error(1948): java.io.InvalidClassException: android.widget.ImageView; IllegalAccessException How deserialize object correctly?

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• which collection should I use

  - by Masna

  Hello, I have a number of custom objects of type X. X has a number of parameters and must be unique in the collection. (I created my own equals method based on the custom parameters to examine this) In each object of type x, I have a list of objects y. I want to add/remove/modify easily an object y. For example: To write the add method, it would be something like add(objTypeX, objTypeY) I would check or the collections already has a objTypeX. If so: i would add the objTypeY to the already existing objTypeX else: i would create objTypeX and add objTypeY to this object. To modify an objTypeY, it would be something like(objTypeX, objTypeY, newobjTypeY) I would get objTypeX out of the collections and modify objTypeY to newobjTypeY Which collections should I use? I tried with hashset but i can get a specific object out of the list, without run down the list till I find that object. I develop this in vb.net 3.5

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• WPF MVVM Pattern - References

  - by KroaX

  Hi everyone I wanted to know if some of you guys can post some articles, blog posts etc. that explain the MVVM Pattern in detail. There are not much explainations out there I think ( except Tutorials). I'm going to write my exam about WPF and also want to build in the MVVM Pattern. So I need some good references that are also digging a little deeper. I think I already have read a lot of texts about MVVM, but maybe you guys got some I didn't read yet. Would really appreciate if you would share your links to good and worth reading articles and explanations

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• Mac dashboard widgets not loading external images

  - by andrhamm

  I set out to make a quick Mac OS X dashboard widget. I read the documentation and was pleased to find out they use simple HTML, JS, and CSS. I created my widget and it works when I open the .html file in Firefox, but it does not work when I install the widget to the dashboard. The widget is simple: it displays the most recent image from a weather web cam stream. The image URLs look like this: http://webcam.com/stream.jpg?1274213999617. The timestamp is appended to the URL and the server automatically responds with the latest image for that time. I did not write the server script. The widget appears to be loading correctly, but the web cam image will not load. Notice the blue question mark in the upper left. The image should appear over the square background image. Is there any special procedure for loading external images into a widget?

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• Materialized Query Table in SQL Server 2005

  - by Azho KG

  In DB2 there is a support for Materialized Query Table (MQT). Basicly you write a query and create a MQT. But the difference from View is that the query is pre-executed and resulting data is stored in MQT and there are some options when to refresh/syncronize the MQT with base tables. I want same functionality in SQL Server. Is there a way to achieve same result? I've tables with millions of rows, and I want to show summary (like total # of members, total expense and etc) in dashboard. So I don't want to count every time user gets to dashboard, instead I want to store them in table and I want that table to be refresh each night. Any kind of hints, answers,suggestions and ideas are welcome. Thanks.

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• Do I always have to supply Tkx's -command argument with an anonymous subroutine?

  - by Zaid

  I find it a bit weird that I have to wrap defined subroutines anonymously when specifying the -command argument for Tkx widgets. The example from TkDocs demonstrates this: my $cb = $frm->new_ttk__button ( -text => "Calculate", -command => sub {calculate();} ); sub calculate { $meters = int(0.3048*$feet*10000.0+.5)/10000.0 || ''; } Why doesn't it work when I write -command => &calculate() or -command => \&calculate()?

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• How to dynamically replace a method implementation in ObjC2?

  - by Abhi

  I am trying to learn how to write plugins using SIMBL. I got my plugin to load with the target application, and also know the method that I wish to override. However, I am not able to use class_getInstanceMethod correctly based on snippets on the Internet. Have things changed in OSX 10.6 and/or ObjC2? The following code from culater.net gives "Dereferencing pointer to incomplete type" on the second-last statement: BOOL DTRenameSelector(Class _class, SEL _oldSelector, SEL _newSelector) { Method method = nil; // First, look for the methods method = class_getInstanceMethod(_class, _oldSelector); if (method == nil) return NO; method->method_name = _newSelector; return YES; } Is there a complete example of how to override a method using SIMBL plugins? Thanks!

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• Vim html.erb snippets?? snipMate Need a vim tip!

  - by Daniel Upton

  Hi, I've started using Vim for my rails development (who hasn't!).. And i'm loving it except that when im in a html.erb file (HTML and Ruby).. I get no snipMate snippets, I would like both html and ruby... or just html would be fine, How would i do this? Would i need to write a set of snippets? if so is there a way of pulling in existing snippets without copying them? Is there a way of telling vim to go into html mode when it sees .html erb? Thanks Daniel

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• click li, go to next li

  - by steve

  Can't find a simple solution to this, I know it's easy and I've tried a few things but I can't quite get it to work. I'm currently working with a sidescrolling site and I want every time you click an image (contained in an li) it scrolls to the next li. I have jQuery plugin localscroll so it smoothly goes from one to the next, and that's working. I need to now write a code that triggers jQuery to utilize the localscroll function and go to the next li. Right now I have this, but I know it's not right: $(document).ready(function () { var gallery = $('.wrapper ul li') $(gallery).click(function() { $.localscroll().next(li); }); });

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• strange problem with WriteBeginTag

  - by user276640

  i use such code, but it renders with error <li class="dd0"><div id="dt1"<a href="http://localhost:1675/Category/29-books.aspx">Books</a></div></li> there is no > in opening tag div. what the problem? writer.WriteBeginTag("li"); //writer.WriteAttribute("class", this.CssClass); writer.WriteAttribute("class", "dd0"); if (!String.IsNullOrEmpty(this.LiLeftMargin)) { writer.WriteAttribute("style", string.Format("margin-left: {0}px", this.LiLeftMargin)); } writer.Write(HtmlTextWriter.TagRightChar); writer.WriteBeginTag("div"); writer.WriteAttribute("id", "dt1"); this.HyperLink.RenderControl(writer); writer.WriteEndTag("div"); writer.WriteEndTag("li");

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• Is there anyway to enable MultiSelect in the StyledTextCtrl

  - by John Baker

  I've noticed that the StyledTextControl (Scintilla basically) in wxWidgets has a great feature that allows multi-selections of text, just like TextMate. However wxRuby doesn't seem to have the function calls to support that feature. I'm wonder if there is a way to enable it or if there might be a way I could rewrite that wrapper to include that function. It seems strange that they would purposely omit that since they are seemingly pretty exhaustive on most functions calls. Any insight on this would be greatly appreciated. I'm trying to write an open source TextMate clone in Ruby and it's gonna be pretty hard without MultiSelect, I could probably hack something together but it'd be ugly. Thanks ahead of time.

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