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• Replacing .NET WebBrowser control with a better browser, like Chrome?

  - by Sylverdrag

  Is there any relatively easy way to insert a modern browser into a .NET application? As far as I understand, the WebBrowser control is a wrapper for IE, which wouldn't be a problem except that it looks like it is a very old version of IE, with all that entails in terms of CSS screw-ups, potential security risks (if the rendering engine wasn't patched, can I really expect the zillion buffer overflow problems to be fixed?), and other issues. I am using Visual Studio C# (express edition - does it make any difference here?) I would like to integrate a good web browser in my applications. In some, I just use it to handle the user registration process, interface with some of my website's features and other things of that order, but I have another application in mind that will require more err... control. I need: A browser that can integrate inside a window of my application (not a separate window) A good support for CSS, js and other web technologies, on par with any modern browser Basic browser functions like "navigate", "back", "reload"... Liberal access to the page code and output. I was thinking about Chrome, since it comes under the BSD license, but I would be just as happy with a recent version of IE. As much as possible, I would like to keep things simple. The best would be if one could patch the existing WebBrowser control, which does already about 70% of what I need, but I don't think that's possible. I have found an activeX control for Mozilla (http://www.iol.ie/~locka/mozilla/control.htm) but it looks like it's an old version, so it's not necessarily an improvement. I am open to suggestions

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• Go: using a pointer to array

  - by Sean

  I'm having a little play with google's Go language, and I've run into something which is fairly basic in C but doesn't seem to be covered in the documentation I've seen so far When I pass a pointer to an array to a function, I presumed we'd have some way to access it as follows: func conv(x []int, xlen int, h []int, hlen int, y *[]int) for i := 0; i<xlen; i++ { for j := 0; j<hlen; j++ { *y[i+j] += x[i]*h[j] } } } But the Go compiler doesn't like this: sean@spray:~/dev$ 8g broke.go broke.go:8: invalid operation: y[i + j] (index of type *[]int) Fair enough - it was just a guess. I have got a fairly straightforward workaround: func conv(x []int, xlen int, h []int, hlen int, y_ *[]int) { y := *y_ for i := 0; i<xlen; i++ { for j := 0; j<hlen; j++ { y[i+j] += x[i]*h[j] } } } But surely there's a better way. The annoying thing is that googling for info on Go isn't very useful as all sorts of C\C++\unrelated results appear for most search terms.

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• Form values in a list item

  - by Tri

  Here is the site mock-up I'm working on for my job: http://dev.arm.gov/~noensie/dqhands/cgi-bin/explorer. I'm still a novice in web developing and I need help with placing form values in a list item to pass on to another page. I'd rather not go in great detail the purpose of this website, but in terms of its basic use, select the parameters in the middle column for a request and add it to the list on the right column by pressing on "add request" button when it appears. After the list have been populated, a user would submit the selected requests, which will direct them to another page based on the requests selected (or added to the list, same thing). That last sentence is where I'm having a problem. Right now, each of request in the list in the right column are <li> elements and I assign them attribute values that needed to be passed on to the next page. I tried inserting a hidden input with same values, but I'm still not sure how to utilize that; I'm not even sure using the hidden input is the correct way. Also the "submit request" button is located outside the <form> block. I was going to utilize javascript and jQuery to enable the button to serialize the values in the <form> block, but I don't know quite how to do that. Go ahead and take a look at my javascript code (index.js) and slay me, or, I mean, my code. It's still pretty elementary and short (~260 lines, that's short right?). I will take any help for this problem (as the matter of fact, if you see any other problems or a better way of implementation of something, go ahead and mention that too); tips, advice, code samples, or whatever else you can contribute, it will be greatly appreciated. Tri

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• How to count term frequency for set of documents?

  - by ManBugra

  i have a Lucene-Index with following documents: doc1 := { caldari, jita, shield, planet } doc2 := { gallente, dodixie, armor, planet } doc3 := { amarr, laser, armor, planet } doc4 := { minmatar, rens, space } doc5 := { jove, space, secret, planet } so these 5 documents use 14 different terms: [ caldari, jita, shield, planet, gallente, dodixie, armor, amarr, laser, minmatar, rens, jove, space, secret ] the frequency of each term: [ 1, 1, 1, 4, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1 ] for easy reading: [ caldari:1, jita:1, shield:1, planet:4, gallente:1, dodixie:1, armor:2, amarr:1, laser:1, minmatar:1, rens:1, jove:1, space:2, secret:1 ] What i do want to know now is, how to obtain the term frequency vector for a set of documents? for example: Set<Documents> docs := [ doc2, doc3 ] termFrequencies = magicFunction(docs); System.out.pring( termFrequencies ); would result in the ouput: [ caldari:0, jita:0, shield:0, planet:2, gallente:1, dodixie:1, armor:2, amarr:1, laser:1, minmatar:0, rens:0, jove:0, space:0, secret:0 ] remove all zeros: [ planet:2, gallente:1, dodixie:1, armor:2, amarr:1, laser:1 ] Notice, that the result vetor contains only the term frequencies of the set of documents. NOT the overall frequencies of the whole index! The term 'planet' is present 4 times in the whole index but the source set of documents only contains it 2 times. A naive implementation would be to just iterate over all documents in the docs set, create a map and count each term. But i need a solution that would also work with a document set size of 100.000 or 500.000. Is there a feature in Lucene i can use to obtain this term vector? If there is no such feature, how would a data structure look like someone can create at index time to obtain such a term vector easily and fast? I'm not that Lucene expert so i'am sorry if the solution is obvious or trivial.

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• Using WCF to expose underlying process

  - by Steven

  I think I must be a little dull because I'm having so much difficulty with this. I use WCF for pretty much everything in-house, it's the most appropriate technology. I have a new Silverlight 3 app that is connecting to the WCF service and that's working fine. Where the problem begins is: Because of the expense in creating the objects within this service and the high correlation of individual objects being shared between clients I want to have a console application that basically gathers/calculates/caches all the data for the service 24/7 and the service basically connects to the console app (or whatever it is) and gets the pre-processed data. eg, think of it in terms of a stock reporting app (which it is). Person A has a portfolio of x, y z Person B has a portfolio of x, q, z, r The service needs to provide updated metrics on how their portfolio is performing. So instead of every 1 second processing person A, then person B, the app independently gathers the stock price and persons position information into memory and the service just queries the in memory result. Thanks for your help, I really am feeling dumb right now.

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• [C#][XNA 3.1] How can I host two different XNA windows inside one Windows Form?

  - by secutos

  I am making a Map Editor for a 2D tile-based game. I would like to host two XNA controls inside the Windows Form - the first to render the map; the second to render the tileset. I used the code here to make the XNA control host inside the Windows Form. This all works very well - as long as there is only one XNA control inside the Windows Form. But I need two - one for the map; the second for the tileset. How can I run two XNA controls inside the Windows Form? While googling, I came across the terms "swap chain" and "multiple viewports", but I can't understand them and would appreciate support. Just as a side note, I know the XNA control example was designed so that even if you ran 100 XNA controls, they would all share the same GraphicsDevice - essentially, all 100 XNA controls would share the same screen. I tried modifying the code to instantiate a new GraphicsDevice for each XNA control, but the rest of the code doesn't work. The code is a bit long to post, so I won't post it unless someone needs it to be able to help me. Thanks in advance.

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• Display gridview in new window

  - by Ricardo Deano

  Hello all. Just a bit of advice needed really in terms of how I should handle my current scenario: I have a web page that searches for products/category information the results of which are at present displayed in a gridview on the same page. However, said gridview is a bit of a beast and as such, I would like to have a page that the user searches for, a button is pressed and the subsequent gridview is displayed in a new window. Ultimately, I would like the user to be able to make multiple searches so that new windows can have multiple gridviews containing different data sets. My current thinking is to create session variables that can be pulled through onto 'the gridview page'. Having said that, I'm not sure that would work if multiple searches are created? I am also thinking I might be able to create said 'gridview window' using javascript but my concern here is the potential loss of functionality of the gridview i.e. paging, sorting, editing, etc. Does anyone have any thoughts or theories on this? What would be "best practise"? Any thoughts greatly appreciated and taken on board. PS: This is being developed in .net, using c# and LINQ. PPS: I'm a noob so be gentle!!

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• Google Maps API - Get points along route between lat/long

  - by user311374

  I have a web site that I am trying to get completed and I need to have the user click points on a map and then work out the route on the roads between the two points. So the user clicks the first point on 1st street, and then clicks another point on 4th street, and the map will find the best way to get there and plot the route on the map. I am assuming this can be done using directions and parse it up, but I have been searching for an hour now and can't find what I am looking for (maybe bad search terms). I need to be able to plot the map manually (?) so I can calculate the distance, etc... of the route as the user continues to click. The site that is in beta is http://www.RunMyRoute.com/UserRoutes/Create and you can see I am trying to create running routes. I want the user to have the option for the route to follow the roads versus just a straight line between two points on the map. Any help on this would be great! Simon.

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• Add new SVN "repo" in poorly constructed repo/project setup

  - by Dave Masselink

  Unfortunately, the answer to this question isn't quite as simple as it sounds... but I hope it can still be relatively simple. Please read all the way through before telling me that the answer is: "svnadmin create... duh" I'm working for a company that set up their SVN server in an odd way (at least in terms of what I'm used to). We've all been there, right? Rather than giving each project a separate repository... they have a folder on the server called "/var/www/svn/repos/" which is the actual SVN repo (has conf/, db/, README.txt, etc. in it). Then they distinguish their projects by adding top level folders into the ONE repository (ex: Project1, Project2, etc.) I don't like this setup and might one day get around to converting the setup to what I'm used to, where each project is its own repository (with separate logs, dbs, etc.) But my question is this: What is the best way to add a new empty project to the current setup? Is there anyway to add a new top level folder/project to the repo through use of svnadmin? It can/should just be an empty folder that I'll start building a new project in. I know that I could do this by checking out the whole singular repository and then adding a new top level folder into my local checkout, then re-committing. But I'd really prefer not to do this because someone has created folders/projects that are just GBs of log data... and I don't want to wait through the download of this just to add a single empty folder. Let me know if there is any more info you'd need to know. I do have root/sudo access on the server in question. Thanks in advance for your help! Dave

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• DDD and MVC: Difference between 'Model' and 'Entity'

  - by Nathan Loding

  I'm seriously confused about the concept of the 'Model' in MVC. Most frameworks that exist today put the Model between the Controller and the database, and the Model almost acts like a database abstraction layer. The concept of 'Fat Model Skinny Controller' is lost as the Controller starts doing more and more logic. In DDD, there is also the concept of a Domain Entity, which has a unique identity to it. As I understand it, a user is a good example of an Entity (unique userid, for instance). The Entity has a life-cycle -- it's values can change throughout the course of the action -- and then it's saved or discarded. The Entity I describe above is what I thought Model was supposed to be in MVC? How off-base am I? To clutter things more, you throw in other patterns, such as the Repository pattern (maybe putting a Service in there). It's pretty clear how the Repository would interact with an Entity -- how does it with a Model? Controllers can have multiple Models, which makes it seem like a Model is less a "database table" than it is a unique Entity. So, in very rough terms, which is better? No "Model" really ... class MyController { public function index() { $repo = new PostRepository(); $posts = $repo->findAllByDateRange('within 30 days'); foreach($posts as $post) { echo $post->Author; } } } Or this, which has a Model as the DAO? class MyController { public function index() { $model = new PostModel(); // maybe this returns a PostRepository? $posts = $model->findAllByDateRange('within 30 days'); while($posts->getNext()) { echo $posts->Post->Author; } } } Both those examples didn't even do what I was describing above. I'm clearly lost. Any input?

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• Would it be possible to have a UTF-8-like encoding limited to 3 bytes per character?

  - by dan04

  UTF-8 requires 4 bytes to represent characters outside the BMP. That's not bad; it's no worse than UTF-16 or UTF-32. But it's not optimal (in terms of storage space). There are 13 bytes (C0-C1 and F5-FF) that are never used. And multi-byte sequences that are not used such as the ones corresponding to "overlong" encodings. If these had been available to encode characters, then more of them could have been represented by 2-byte or 3-byte sequences (of course, at the expense of making the implementation more complex). Would it be possible to represent all 1,114,112 Unicode code points by a UTF-8-like encoding with at most 3 bytes per character? If not, what is the maximum number of characters such an encoding could represent? By "UTF-8-like", I mean, at minimum: The bytes 0x00-0x7F are reserved for ASCII characters. Byte-oriented find / index functions work correctly. You can't find a false positive by starting in the middle of a character like you can in Shift-JIS.

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• How to non-greedy multiple lookbehind matches

  - by ArtK

  Source: <prefix><content1><suffix1><prefix><content2><suffix2> Engine: PCRE RegEx1: (?<=<prefix>)(.*)(?=<suffix1>) RegEx2: (?<=<prefix>)(.*)(?=<suffix2>) Result1: <content1> Result2: <content1><suffix1><prefix><content2> The desired result for RegEx2 is just <content2> but it is obviously greedy. How do I make RegEx2 non-greedy and use only the last matching lookbehind? [I hope I have translated this correctly from the NoteTab syntax. I don't do much RegEx coding. The <prefix>, <content> & <suffix> terms are just meant to represent arbitrary strings. Only the "<" in the "?<=" lookbehind command is significant.] I suspect it is something simple but after too many hours of searching I'm giving up on solving it myself. Thanks for the help Art

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• Managing/Storing complex application form

  - by mickyjtwin

  I am developing an online application form, which can be of two categories, either domestic/international. Each different type has commong questions, and also specific questions. They are approx 6 pages/steps of questions. The application form can also be saved at the end of each step, and can be completed at a later date. Some questions will vary depending on answers to previous questions, so there are some complex business rules. In terms of storage of results, would it be best to store the answers in and XML field in SQL? What would be the best way to reference a question to an answer. There is no need for the form to be dynamic in rendering questions etc. e.g. <Application id="123" type="Domestic"> <Answers> <EmailAddress>[email protected]</EmailAddress> <HomePhone>555-5555</HomePhone> <Suburb>MySuburb</Suburb> <Guardians> <Guardian type="Mother"> <FirstName>Mom</FirstName> </Guardian> </Guardians> <Answers> </Application>

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• JBoss: What does the warning EJBTHREE-1246 from the InterceptorRegistry mean?

  - by Simon Lehmann

  I am currently developing an EJB 3.0 based application on the JBoss AS 5.0.0.GA and just recently the following warning showed up in the server log: 09:50:19,735 WARN [InterceptorsFactory] EJBTHREE-1246: Do not use InterceptorsFactory with a ManagedObjectAdvisor, InterceptorRegistry should be used via the bean container 09:50:19,735 WARN [InterceptorsFactory] EJBTHREE-1246: Do not use InterceptorsFactory with a ManagedObjectAdvisor, InterceptorRegistry should be used via the bean container 09:50:19,735 WARN [InterceptorRegistry] applicable interceptors is non-existent for ... ... The warnings are generated as soon as an EJB (a stateless session bean) is injected into a backing bean of my JSF web-application. The beans do work without problems though, but I still would like to know where that warning comes from and what I can do to avoid it. I have already searched a bit around, but haven't found a good answer (some say, bean developers do not have to worry, but its a warning, so I'd like to have a better solution): http://www.jboss.com/index.html?module=bb&op=viewtopic&t=147292 http://www.jboss.com/index.html?module=bb&op=viewtopic&p=4180366 http://www.jboss.com/index.html?module=bb&op=viewtopic&p=4140136 JBoss JIRA Issue about the warning (Not that helpful in my opinion) So has anyone an explanation what causes the warning (in terms of a bean developer, not application server developer) and what to do to avoid it? Update: I've just upgraded JBoss to 5.0.1.GA (Download, Release-Notes) but unfortunatly the warning still appears.

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• Packaging reference documentation with jar file

  - by soren.enemaerke

  We are porting our .NET library to a java equivalent and is now looking at how to distribute this port. Packaging the classes into a jar-file seems like best practice and we would then ship this jar file in a zip along with some license terms. But what about the documentation? In .NET land it seems like best practice to distribute the xml file that can be consumed by tooling (Visual Studio) but we can't seem to find such best practices for java. We have javadoc comments on our public classes and interfaces, so we are just looking for a way to generate and distribute these comments in a way that is developer friendly (we're thinking easily consumed from various IDEs). What are developers expecting and how do you best deliver this? We would really prefer to bundle the documentation along with the jar file and not have to host the documentation on our website EDIT: We would like for our documentation to appear inside the java IDEs so we want to provide the documentation in a way that integrates into the IDEs as gracefully as possible. In .NET land this is as an xml file placed next to the .dll file, but is there a similar concept for jar files that enables the integration into tooling? PS: We are developing in Eclipse and have an ant task doing the building and jar-file packaing in our automated build.

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• Python Post Upload JPEG to Server?

  - by iJames

  It seems like this answer has been provided a bunch of times but in all of it, I'm still getting errors from the server and I'm sure it has to do with my code. I've tried HTTP, and HTTPConnection from httplib and both create quite different terminal outputs in terms of formatting/encoding so I'm not sure where the problem lies. Does anything stand out here? Or is there just a better way? Pieced together from an ancient article because I really needed to understand the basis of creating the post: http://code.activestate.com/recipes/146306-http-client-to-post-using-multipartform-data/ Note, the jpeg is supposed to be "unformatted". The pseudocode: boundary = "somerandomsetofchars" BOUNDARY = '--' + boundary CRLF = '\r\n' fields = [('aspecialkey','thevalueofthekey')] files = [('Image.Data','mypicture.jpg','/users/home/me/mypicture.jpg')] bodylines = [] for (key, value) in fields: bodylines.append(BOUNDARY) bodylines.append('Content-Disposition: form-data; name="%s"' % key) bodylines.append('') bodylines.append(value) for (key, filename, fileloc) in files: bodylines.append(BOUNDARY) bodylines.append('Content-Disposition: form-data; name="%s"; filename="%s"' % (key, filename)) bodylines.append('Content-Type: %s' % self.get_content_type(fileloc)) bodylines.append('') bodylines.append(open(fileloc,'r').read()) bodylines.append(BOUNDARY + '--') bodylines.append('') #print bodylines content_type = 'multipart/form-data; boundary=%s' % BOUNDARY body = CRLF.join(bodylines) #conn = httplib.HTTP("www.ahost.com") # In both this and below, the file part was garbling the rest of the body?!? conn = httplib.HTTPConnection("www.ahost.com") conn.putrequest('POST', "/myuploadlocation/uploadimage") headers = { 'content-length': str(len(body)), 'Content-Type' : content_type, 'User-Agent' : 'myagent' } for headerkey in headers: conn.putheader(headerkey, headers[headerkey]) conn.endheaders() conn.send(body) response = conn.getresponse() result = response.read() responseheaders = response.getheaders() It's interesting in that the real code I've implemented seems to work and is getting back valid responses, but the problem it it's telling me that it can't find the image data. Maybe this is particular to the server, but I'm just trying to rule out that I'm not doing some thing exceptionally stupid here. Or perhaps there's other methodologies for doing this more efficiently. I've not tried poster yet because I want to make sure I'm formatting the POST correctly first. I figure I can upgrade to poster after it's working yes?

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• web design question (php/ajax)

  - by tom smith

  Hi guys... Hope this isn't a waste of your time. I'm working on a project, and it occured to me that there's a chunk of code out there, that should allow me to see how others have implemented this. I've got a project where I'm going to have a page, with a sel box. the user will select an item from the selList, and based on the item selected, a separate section of the page (areaB) will change in terms of the content/tbls being displayed. i then want to allow the user to go through a series of subpages in areaB, where the user goes through a submit/cancel/confirm process, where the stuff in areaB changes, with the rest of the page remaining the same... i'm trying to figure out the best approach to implement the on both client/server side. i could just have an ugly "if block" where i have abunch of logic, and i completely regen the page each time the user selects an action.. i could have an approach that might involve divs/frames, where i then just regen the targeted frame/div area.. is this even possible?? i could have some form of ajaxy process, which would only alter the targeted section(s) of the page... so.. i'm trying to talk to anyone who has ideas on how to do this, or more ideally, if you know of a good code (client/server) side example of this... that i can examine. i'd really appreciate it!! i've got a more detailed overview but didn't know if it would be cool to post it here... thanks.. tom

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• Automated UAT/functional tests on Swing applications without source code

  - by jas

  Our team is now working on a big Swing application. Our job basically focuses on writing extensions to the existing framework. A typical job would be adding a new panel/ or adding a new tab with some extra functionalities that suit our need. It seems FEST can help a lot in terms of unit-test our code. I am going to try it out this week. But the question here is if there is a way to do automated functional testing on the whole application. In another word, we do not only need to test our code but also the framework. After all, UAT is the most important part. I am currently considering decompiling the jar files we got into source code then we can identify the components and then use FEST. So, before I get started to give this approach a shot, I think I just ask for ideas and inspirations here. There must be people who have done similar things before. Would be nice if I could learn from the veterans who fought against this before . Thanks,

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• Get Chinese Romanization from Google Translate API

  - by krubo

  The Google language translate API works cleanly to translate into Chinese: <script type="text/javascript" src="http://www.google.com/jsapi"></script> <script> google.load('language','1'); function googletrans(text) { google.language.translate(text,'en','zh',function(result) { alert(result.translation); }); } </script> <input onchange="googletrans(this.value);"> Example input: "Hello" Result: "??" My problem is I can't get the Romanization (pronunciation using English letters). This is a known issue. Now the data is right there on translate.google.com (Example input: "Hello" Result: "Ni hao") and I can even see it by pointing my browser to: http://translate.google.com/translate_a/t?client=t&text=hello&hl=en&sl=en&tl=zh-CN&otf=2&pc=0 Result: {"sentences":[{"trans":"??","orig":"hello","translit":"Ni hao"}], "dict":[{"pos":"interjection","terms":["?"]}],"src":"en"} But somehow when I try to get this URL with ajax it fails (XMLHttpRequest Exception 101). Is there any way to retrieve this Romanization data with ajax?

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• Code bacteria: evolving mathematical behavior

  - by Stefano Borini

  It would not be my intention to put a link on my blog, but I don't have any other method to clarify what I really mean. The article is quite long, and it's in three parts (1,2,3), but if you are curious, it's worth the reading. A long time ago (5 years, at least) I programmed a python program which generated "mathematical bacteria". These bacteria are python objects with a simple opcode-based genetic code. You can feed them with a number and they return a number, according to the execution of their code. I generate their genetic codes at random, and apply an environmental selection to those objects producing a result similar to a predefined expected value. Then I let them duplicate, introduce mutations, and evolve them. The result is quite interesting, as their genetic code basically learns how to solve simple equations, even for values different for the training dataset. Now, this thing is just a toy. I had time to waste and I wanted to satisfy my curiosity. however, I assume that something, in terms of research, has been made... I am reinventing the wheel here, I hope. Are you aware of more serious attempts at creating in-silico bacteria like the one I programmed? Please note that this is not really "genetic algorithms". Genetic algorithms is when you use evolution/selection to improve a vector of parameters against a given scoring function. This is kind of different. I optimize the code, not the parameters, against a given scoring function.

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• Why does ANTLR not parse the entire input?

  - by Martin Wiboe

  Hello, I am quite new to ANTLR, so this is likely a simple question. I have defined a simple grammar which is supposed to include arithmetic expressions with numbers and identifiers (strings that start with a letter and continue with one or more letters or numbers.) The grammar looks as follows: grammar while; @lexer::header { package ConFreeG; } @header { package ConFreeG; import ConFreeG.IR.*; } @parser::members { } arith: term | '(' arith ( '-' | '+' | '*' ) arith ')' ; term returns [AExpr a]: NUM { int n = Integer.parseInt($NUM.text); a = new Num(n); } | IDENT { a = new Var($IDENT.text); } ; fragment LOWER : ('a'..'z'); fragment UPPER : ('A'..'Z'); fragment NONNULL : ('1'..'9'); fragment NUMBER : ('0' | NONNULL); IDENT : ( LOWER | UPPER ) ( LOWER | UPPER | NUMBER )*; NUM : '0' | NONNULL NUMBER*; fragment NEWLINE:'\r'? '\n'; WHITESPACE : ( ' ' | '\t' | NEWLINE )+ { $channel=HIDDEN; }; I am using ANTLR v3 with the ANTLR IDE Eclipse plugin. When I parse the expression (8 + a45) using the interpreter, only part of the parse tree is generated: http://imgur.com/iBaEC.png Why does the second term (a45) not get parsed? The same happens if both terms are numbers. Thank you, Martin Wiboe

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• How can I apply a PSSM efficiently?

  - by flies

  I am fitting for position specific scoring matrices (PSSM aka Position Specific Weight Matrices). The fit I'm using is like simulated annealing, where I the perturb the PSSM, compare the prediction to experiment and accept the change if it improves agreement. This means I apply the PSSM millions of times per fit; performance is critical. In my particular problem, I'm applying a PSSM for an object of length L (~8 bp) at every position of a DNA sequence of length M (~30 bp) (so there are M-L+1 valid positions). I need an efficient algorithm to apply a PSSM. Can anyone help improve performance? My best idea is to convert the DNA into some kind of a matrix so that applying the PSSM is matrix multiplication. There are efficient linear algebra libraries out there (e.g. BLAS), but I'm not sure how best to turn an M-length DNA sequence into a matrix M x 4 matrix and then apply the PSSM at each position. The solution needs to work for higher order/dinucleotide terms in the PSSM - presumably this means representing the sequence-matrix for mono-nucleotides and separately for dinucleotides. My current solution iterates over each position m, then over each letter in word from m to m+L-1, adding the corresponding term in the matrix. I'm storing the matrix as a multi-dimensional STL vector, and profiling has revealed that a lot of the computation time is just accessing the elements of the PSSM (with similar performance bottlenecks accessing the DNA sequence). If someone has an idea besides matrix multiplication, I'm all ears.

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• Invert a string: Recursion vs iteration in javascript

  - by steweb

  Hi all, one month ago I've been interviewed by some google PTO members. One of the questions was: Invert a string recursively in js and explain the running time by big O notation this was my solution: function invert(s){ return (s.length > 1) ? s.charAt(s.length-1)+invert(s.substring(0,s.length-1)) : s; } Pretty simple, I think. And, about the big-o notation, I quickly answered O(n) as the running time depends linearly on the input. - Silence - and then, he asked me, what are the differences in terms of running time if you implement it by iteration? I replied that sometimes the compiler "translate" the recursion into iteration (some programming language course memories) so there are no differences about iteration and recursion in this case. Btw since I had no feedback about this particular question, and the interviewer didn't answer "ok" or "nope", I'd like to know if you maybe agree with me or if you can explain me whether there could be differences about the 2 kind of implementations. Thanks a lot and Regards!

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• Http Digest Authentication, Handle different browser char-sets...

  - by user160561

  Hi all, I tried to use the Http Authentication Digest Scheme with my php (apache module) based website. In general it works fine, but when it comes to verification of the username / hash against my user database i run into a problem. Of course i do not want to store the user´s password in my database, so i tend to store the A1 hashvalue (which is md5($username . ':' . $realm . ':' . $password)) in my db. This is just how the browser does it too to create the hashes to send back. The Problem: I am not able to detect if the browser does this in ISO-8859-1 fallback (like firefox, IE) or UTF-8 (Opera) or whatever. I have chosen to do the calculation in UTF-8 and store this md5 hash. Which leads to non-authentication in Firefox and IE browsers. How do you solve this problem? Just do not use this auth-scheme? Or Store a md5 Hash for each charset? Force users to Opera? (Terms of A1 refer to the http://php.net/manual/en/features.http-auth.php example.) (for digest access authentication read the according wikipedia entry)

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• addChild, etc. using NSTreeController and NSTreeNode (snow leopard)

  - by John Velman

  I have a setup with an object (OTNodeDatum) (OT for OutlineTest) to be the represented object in NSTreeNode. NSTreeNode is the Class shown in the attributes page for NSTreeController. I have document based app, no core data. On MyDocument init, I set up content with an NSMutableArray containing one item, an NSTreeNode with a represented object which contains a single property (yes, name). Add button, Add Child button, Delete button, hooked up via interface builder to the NSTreeController add action, etc. It works up to a point. When I do an add, I get a new blank line which I can edit, but the inserted text goes away when I leave the cell. When I do a delete, things get deleted. When I do add child, nothing happens. I think I have to subclass either NSTreeNode, or NSTreeController to get the right behavior in terms of adding children and adding a new represented object in addition to adding a new tree node. IS this on the right track? If I subclass NSTreeController would I just override the add, addChild, to get the right thing to happen? And what could I mess up? I can't seem to find any guidance on this, although I've spent a long time looking. Thanks. John V

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