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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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  • N-son tabbed/JsScrollbar, trying to force gif play from click of link using jquery

    - by user314286
    Hello everyone, Let me start off by stating the obvious; I am new here. That said I hope I am not violating some standard I missed by posting this. xD For several days now I've been trying to update a rather old site of mine, to which I wont link to given that the update is so drastic that the current product on which I seek your help for doesn't resemble the old site in any other way then appearance. Anywho! I am using the tabbed div and JsScrollbar created by N-son (http://www.downloadjavascripts.com/list/javasitek60/Details.aspx) and so far have only used jquery to dynamically center content on the page. My problem however is this...I have a gif on the page that acts as a background (it's not tiled) and I'd like to be able to have it so that when you click on one of the links used in n-sons tabs (EX: news) it also causes the gif to load and play through itself once. So far all my attempts at accomplishing this myself have failed and break wither the scrollbar or prevent the content from switching when you click the tabs. (Except for one failed attempt where it all worked fine except the handle for the scrollbar would vanish upon switching tabs) I hope I've been clear in this and that someone is able to help. I know it may seem like a silly question but we're all new at some point. :P If need be I'll upload what coding I have but it is not pretty. Thank you in advance.

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  • What is the best method for implementing mouse wheel activity in Delphi VCL forms?

    - by Brian Frost
    As a long time user of Delphi 7, I've rolled my own mouse wheel handling in a few controls but lately I've noticed that some recent applications only need the mouse cursor to be placed over a control (e.g a list box or tree view) for the mouse wheel activity to cause that control to scroll. This feels nice (as opposed to having to click focus a control before it responds to the wheel. Now I've moved to Delphi 2010 I'm wondering what is the 'correct' behavior? And what can I use in Delphi that avoids me having to bodge this with my own solutions now? Thanks.

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  • How to use Visual Studio debugger visualizers built against a different framework version?

    - by michielvoo
    I compiled the ExpressionTreeVisualizer project found in the Visual Studio 2010 samples but when I try to use it in a .NET 3.5 project I get the exception below: Could not load file or assembly 'file:///C:\Program Files (x86)\Microsoft\Visual Studio 2010\Common7\Packages\Debugger\Visualizers\ExpressionTreeVisualizer.dll' or one of its dependencies. This assembly is built by a runtime newer than the currently loaded runtime and cannot be loaded. The sample project had the TargetFrameworkVersion set to v4.0 and after changing it to v3.5 and building it now works in my project. I changed the source code and project file and rebuilt it so that I now have two expression tree visualizers, one for v3.5 projects and one for v4.0 projects. Is there a better way? Thanks!

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  • Which GUI control is suitable for this purpose?

    - by pecker
    Hello, I'm using winforms of .NET & C#. I'm developing a medical software. I need to implement "Patient History". When doctor enters the PatientID. All the previous appointment dates will be displayed in a side panel. These entries will dynamically fetched from the database. Interface will be more or less similar to Histroy in web browser. Except that I'm not going to use tree control and categorize entries into 'today' 'yesterday' 'older than 7 days' 'last week' etc.. What controls do I need to use. I'm not clear about this. If you have any better idea. Please mention.

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  • Code editor with autocomplete

    - by Andrey
    I need to create a code editor for my own simple language: className.MethodName(parameterName = 2, ... ) I've created the appropriate grammar and autogenerate parser using ANTLR tool. Now I would like to have an autocomplete for class, method, variables and parameter names. This list should be context dependent, f.e. for "class." it should display methods and for "class.Method(" - parameters. I was going to parse the text and display the list depending on in which node the cursor is. The problem is that for incomplete code like "aaa.bbb(" the parser produces an error instead of a syntax tree. Any idea how to solve this problem? Maybe I'm on the wrong way and I shouldn't parse code to display autocomplete?

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  • iPhone SDK: Progressive UITableView updates, smoothly animated

    - by boliva
    Hi all, There's something I've been trying to do with no success. I have an UITableView whose viewController is both its delegate and dataSource. On it I also have a mutableArray as a property, which basically acts as the tableView dataSource. This mutableArray gets continously updated from an online XML source. What I haven't been able to accomplish successfully is to animate the adding of new rows at the top of the tableView and the deletion of the oldest rows at its bottom (thinking I'll always going to show the same amount of data, say the latest 10 entries). The method I'm actually using is that, after finishing receiving and parsing the XML data I'm removing all the contents of the mutableArray and storing the new entries on it, to later reload the tableView (calling the 'reloadData' method). In between I'm using a CATransition in order to 'fade' the tableView from its previous to its new state. I tried using beginUpdates and endUpdates, with code for selectively removing the old rows from the tableView and adding the new ones to it, as well as to its datasource, however the animation takes place in the whole table instead of the affected rows only. What I want to accomplish is, after an update, to delete as many rows from the 'bottom' of the table as new entries I have retrieved, sliding the tableView down and adding the new rows at the top of it, smoothly animated. Best regards,

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  • Override comparison for F# set

    - by Mauricio Scheffer
    Is there any way to override the comparison function in a F# set? I don't see any set construction functions that take a IComparer<T> or comparison function: Set.ofSeq et al don't take a comparison function FSharpSet(IComparer<T> comparer, SetTree<T> tree) constructor is internal, because SetTree is internal and SetTreeModule.ofSeq<a>(IComparer<a> comparer, IEnumerable<a> c) is obviously internal too. My actual problem is that I have a set of ('a * 'a) and I want a comparison such that for example (1,3) = (3,1). I know I could wrap this in a type implementing IComparable<T>, but is there any way to avoid this?

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  • Unit testing opaque structure based C API

    - by Nicolas Goy
    I have a library I wrote with API based on opaque structures. Using opaque structures has a lot of benefits and I am very happy with it. Now that my API are stable in term of specifications, I'd like to write a complete battery of unit test to ensure a solid base before releasing it. My concern is simple, how do you unit test API based on opaque structures where the main goal is to hide the internal logic? For example, let's take a very simple object, an array with a very simple test: WSArray a = WSArrayCreate(); int foo = 5; WSArrayAppendValue(a, &foo); int *bar = WSArrayGetValueAtIndex(a, 0); if(&foo != bar) printf("Eroneous value returned\n"); else printf("Good value returned\n"); WSRelease(a); Of course, this tests some facts, like the array actually acts as wanted with 1 value, but when I write unit tests, at least in C, I usualy compare the memory footprint of my datastructures with a known state. In my example, I don't know if some internal state of the array is broken. How would you handle that? I'd really like to avoid adding codes in the implementation files only for unit testings, I really emphasis loose coupling of modules, and injecting unit tests into the implementation would seem rather invasive to me. My first thought was to include the implementation file into my unit test, linking my unit test statically to my library. For example: #include <WS/WS.h> #include <WS/Collection/Array.c> static void TestArray(void) { WSArray a = WSArrayCreate(); /* Structure members are available because we included Array.c */ printf("%d\n", a->count); } Is that a good idea? Of course, the unit tests won't benefit from encapsulation, but they are here to ensure it's actually working.

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  • Weird behaviour of a deserialized class

    - by orloffm
    I've got a huge XML file that's being deserialized by XmlSerializer in an XSD-generated class structure. Everything used to work just fine, but now a weird thing started happening. Sometimes (50% of runs) a field of a certain object of a class that's deep in the class tree just changes to a certain value of the same field of a different object of the same class. It happens when entering some function, when debugger steps from opening "{" to the first line of code. I understand that it's stupid question, but maybe someone have any thoughts?

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  • wx Python is not properly drawing customtree items

    - by uberjumper
    Hi, I am currently using wx.CustomTree, to use to display a series of configuration settings. I generally fill them with wx.TextCtrl / wx.Combobox, to allow the user to edit / enter stuff. Here is my code: class ConfigTree(CT.CustomTreeCtrl): """ Holds all non gui drawing panel stuff """ def __init__(self, parent): CT.CustomTreeCtrl.__init__(self, parent, id = common.ID_CONTROL_SETTINGS, style = wx.TR_DEFAULT_STYLE | wx.TR_HAS_BUTTONS | wx.TR_HAS_VARIABLE_ROW_HEIGHT | wx.TR_SINGLE) #self.HideWindows() #self.RefreshSubtree(self.root) self.population_size_ctrl = None self.SetSizeHints(350, common.FRAME_SIZE[1]) self.root = self.AddRoot("Configuration Settings") child = self.AppendItem(self.root, "Foo", wnd=wx.TextCtrl(self, wx.ID_ANY, "Lots Of Muffins")) The problem is, any children nodes, the data for these nodes is not filled in. When i basically expand the configuration settings tree node. I see the "Foo" node, however the textbox is empty. This is the same for both text node, Until i actually click on the child node. I've looked tried every form of update / etc. Does anyone have any ideas?

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  • jQuery UI slider coming out looking wierd

    - by jondavidjohn
    http://cl.ly/2W1V3s0G2G3y3D133I3U <--screenshot of rendered slider It acts normally by clicking the inner whitespace of the slider and dragging, values act accordingly, but the handles do not move and fill the area, and the line at the top grows/shrinks with the difference of the two values. Here is the code I am using to initiate the slider. $('.sliderific').each(function(){ alert($(this).attr('id')); $(this).slider({ range: true, min: 0, max: 500, values: [ 75, 300 ], slide: function( event, ui ) { $(this).nextAll('.left:first').text(ui.values[ 0 ]); $(this).nextAll('.right:first').text(ui.values[ 1 ]); } }); }); and here is the DOM it's being applied to... <div class="white notwide"> <div id="price-slider" class="sliderific"></div> <span class="em small gray left center">Min Price</span> <span class="em small gray right center">Max Price </span> </div> EDIT : Also, I have verified I am including the proper css and the jquery theme images are connecting and being loaded.

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  • Building MobileVLCKit from git.videolan.org repository on macOsX with XCode

    - by ztepsic
    I would like to make an application for iOS(iPhone and iPad) that can play streaming videos through RTSP protocol (that includes mms). I imagined to achive a specified application using VLC player or libVLC library. On the official vlc git repository (http://git.videolan.org/?p=vlc.git;a=tree) in projects/macosx/framework/ folder there is xcode project MobileVLCKit.xcodeproj for which I assume that is a somewhat usable VLC framework for iOS. Now the problem is that I can't/don't know how to build this project. When I try to build MobileVLCKit.xcodeproj I get an error that says it can't find files inside extras/contrib/hosts/i686-apple-darwin10/ios/ folder. I have looked within that folder (extras/contrib) and managed to create folder (with files) extras/contrib/hosts/i686-apple-darwin10/ with make, but there is no ios folder. So, does anybody knows how to successfully build MobileVLCKit?

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  • Colouring JTree's TreeNodes

    - by Amadan
    I have a JTree which I give objects that implement the TreeNode interface, and a custom TreeModel to display them (not using DefaultMutableTreeNode). I would like to change the text colour of some nodes. I can't find anything in the docs, except javax.swing.tree.DefaultTreeCellRenderer.setTextNonSelectionColor(Color newColor), but it will change everything indiscriminately, and I only need it for some nodes (specifically, broken links, i.e. nodes whose corresponding files can't be found on the disk, should be greyed out, the rest should be default). Can it be done, and how?

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  • Configuring mod_rewrite and mod_jk for Apache 2.2 and JBoss 4.2.3

    - by The Pretender
    Hello! My problem is as follows: I have JBoss 4.2.3 application server with AJP 1.3 connector running on one host under Windows (192.168.1.2 for my test environment) and Apache 2.2.14 running on another FreeBSD box (192.168.1.10). Apache acts as a "front gate" for all requests and sends them to JBoss via mod_jk. Everything was working fine until I had to do some SEO optimizations. These optimizations include SEF urls, so i decided to use mod_rewrite for Apache to alter requests before they are sent to JBoss. Basically, I nedd to implement 2 rules: Redirect old rules like "http://hostname/directory/" to "http://hostname/" with permanent redirect Forward urls like "http://hostname/wtf/123/" to "http://hostname/wtf/view.htm?id=123" so that end user doesn't see the "ugly" URL (the actual rewrite). Here is my Apache config for test virtual host: <VirtualHost *:80> ServerAdmin [email protected] DocumentRoot "/usr/local/www/dummy" ServerName 192.168.1.10 <IfModule mod_rewrite.c> RewriteEngine On RewriteRule /directory/(.*) /$1 [R=permanent,L] RewriteRule ^/([^/]+)/([0-9]+)/?$ /$1/view.htm?id=$2 </IfModule> JkMount /* jsp-hostname ErrorLog "/var/log/dummy-host.example.com-error_log" CustomLog "/var/log/dummy-host.example.com-access_log" common </VirtualHost> The problem is that second rewrite rule doesn't work. Requests slip through to JBoss unchanged, so I get Tomcat 404 error. But if I add redirect flag to the second rule like RewriteRule ^/([^/]+)/([0-9]+)/?$ /$1/view.htm?id=$2 [R,L] it works like a charm. But redirect is not what I need here :) . I suspect that the problem is that requests are forwarded to the another host (192.168.1.2), but I really don't have any idea on how to make it work. Any help would be appreciated :)

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  • WPF ItemsControl - how to know when the items finished loading, so that I can focus the first one?

    - by Tomáš Kafka
    Hi everyone, I have an ItemsControl in my View, that is bound to an ObservableCollection from ViewModel. The collection is filled, and afterwards an event from VM to view is raised (think search results and SearchFinished event). I would like to move keyboard focus to the first item in an ItemsControl, but when I do it in View's code-behind when handling SearchFinished, the items are not yet rendered (the collection is filled already, but wpf's rendering is asynchronous and didn't happen yet), so there is nothing to focus (Focus() needs to have the items' visual tree already constructed). I wanted to do (myItemsControl.ItemContainerGenerator.ContainerFromIndex(0) as UIElement).Focus();, but as the 0th item is not yet loaded, ContainerFromIndex(0) returns null. I tried delaying it with Dispatcher.BeginInvoke... with low priority, but that is dependent on exact timing and usually doesn't work. How can I wait until the first item in ItemsControl is Loaded?

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  • Drawing Directed Acyclic Graphs: Minimizing edge crossing?

    - by Robert Fraser
    Laying out the verticies in a DAG in a tree form (i.e. verticies with no in-edges on top, verticies dependent only on those on the next level, etc.) is rather simple without graph drawing algorithms such as Efficient Sugimiya. However, is there a simple algorithm to do this that minimizes edge crossing? (For some graphs, it may be impossible to completely eliminate edge crossing.) A picture says a thousand words, so is there an algorithm that would suggest: instead of: EDIT: As the picture suggests, a vertex's inputs are always on top and outputs are always below, which is another barrier to just pasting in an existing layout algorithm.

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  • How to get object properties of specific class in SPARQL

    - by udayalkonline
    hi, I have some ontology(campus.owl).There are tree classes(Student,Sport,Lecturer).Student class is joined with Lecturer class using "has" object property and Student class joined with Sport class with "isPlay" object property. problem I want to get the object property between Student and Lecturer using some SPARQL query. PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema# PREFIX rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# PREFIX my: http://www.semanticweb.org/ontologies/2010/5/Ontology1275975684120.owl# SELECT ?prop WHERE { ?prop ..........??? } Any Idea..?? Thank in advance!

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  • Git subtree workflow

    - by Cedric
    In my current project I'm using an open source forum (https://github.com/vanillaforums/Garden.git). I was planning on doing something like this : git remote add vanilla_remote https://github.com/vanillaforums/Garden.git git checkout -b vanilla vanilla_remote/master git checkout master git read-tree --prefix=vanilla -u vanilla This way I can make change into the vanilla folder (like changing config) and commit it to my master branch and I can also switch into my vanilla branch to fetch updates. My problem is when I try to merge the branch together git checkout vanilla git pull git checkout master git merge --squash -s subtree --no-commit vanilla The problem is that the "update commit" goes on top of my commits and "overwrite" my change. I would rather like to have my commits replay on top of the update. Is there a simple way to do that? I'm not very good in git so maybe this is the wrong approach. Also, I really don't want to mix my history with the vanilla history.

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  • Compressing three individual jpeg pics containing temporal redundancy?

    - by michael
    I am interfacing and embedded device with a camera module that returns a single jpeg compressed frame each time I trigger it. I would like to take three successive shots (approx 1 frame per 1/4 second) and further compress the images into a single file. The assumption here is that there is a lot of temporal redundancy, therefore lots of room for more compression across the three frames (compared to sending three separate jpeg images). I will be implementing the solution on an embedded device in C without any libraries and no OS. The camera will be taking pics in an area with very little movement (no visitors or screens in the background, maybe a tree with swaying branches), so I think my assumption about redundancy is pretty solid. When the file is finally viewed on a pc/mac, I don't mind having to write something to extract the three frames (so it can be a nonstandard cluge) So I guess the actual question is: What is the best way to compress these three images together given the fact that they are already in JPEG format (it is a possibly to convert back to a raw image, but if i dont have too...)

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  • Problem with connection to MS SQL Server database using SSMS

    - by Charles
    I have a database on line with Godaddy (who uses SQL Server 2005). They provide basic management tools, but tell you that for more advanced tools you can connect directly using SSMS. I followed their instructions to ensure my online database will accept remote connections, and can apparently log in using SSMS with success (after giving my hostname and access data). However: When attempting to expand the "Databases" folder tree, I get the following error: Failed to retrieve data for this request. (Microsoft.SqlServer.Management.Sdk.Sfc) For help, click: http://go.microsoft.com/fwlink?ProdName=Microsoft+SQL+Server& LinkId=20476 ADDITIONAL INFORMATION: An exception occurred while executing a Transact-SQL statement or batch. (Microsoft.SqlServer.ConnectionInfo) The server principal "cmitchell" is not able to access the database "3pointdb" under the current security context. (Microsoft SQL Server, Error: 916) For help, click: http://go.microsoft.com/fwlink?ProdName=Microsoft+SQL+Server&ProdVer=09.00.4262&EvtSrc=MSSQLServer&EvtID=916&LinkId=20476

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  • Injecting an XML fragment into the current document from an external file

    - by makenai
    I'm currently parsing an XML file using REXML and trying to come up with a way of inserting an XML fragment from an internal file. Currently, I'm using some logic like the following: doc.elements.each('//include') do |element| handleInclude( element ) end def handleInclude( element ) if filename = element.attributes['file'] data = File.open( filename ).read doc = REXML::Document.new( data ) element.parent.replace_child( element, doc ) end end Where my XML looks like the following: <include file="test.xml" /> But this seems a little bit clunky, and I'm worried that REXML might not always parse XML fragments correctly due to absence of a proper root node in some cases. Is there a better way of doing this? Concern #2: REXML seems not to pick up my changes after I replace elements. For example, after making a change: doc.elements.each('rootNode/*') do |element| end ..picks up neither the original element I replaced, nor the one I replaced it with. Is there some trick to getting REXML to rescan its' tree?

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  • Simplest way to debug an android bluetooth application

    - by intiha
    I am trying to test and build a sample android application that can simply connect to a BT server to send and receive a few packets. Since the emulator has no support what is the next best thing to test BT communication? Can I just run a code that acts as a server on my laptop and dumps BT connection onto a console? Do I have to write this code, or is their a simple tool that saves me that hassle? One more thing, I have windows 7, and currently I attach to my PC an anycom USB BT adapter. This is able to show up my nexus one as a BT device. I can pair to my laptop but connection always fails. When it tries to pair I have tried both 0000 and 1234 as suggested on my nexus, but in my connection list it still lists my laptop as paired but not connected. Any idea why? I searched for this problem and apparently people talk about rebooting and power cycling BT, but these solutions dont work for me. Thanks. Affan.

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  • Using 'git pull' vs 'git checkout -f' for website deployment

    - by Michelle
    I've found two common approaches to automatically deploying website updates using a bare remote repo. The first requires that the repo is cloned into the document root of the webserver and in the post-update hook a git pull is used. cd /srv/www/siteA/ || exit unset GIT_DIR git pull hub master The second approach adds a 'detached work tree' to the bare repository. The post-receive hook uses git checkout -f to replicate the repository's HEAD into the work directory which is the webservers document root i.e. GIT_WORK_TREE=/srv/www/siteA/ git checkout -f The first approach has the advantage that changes made in the websites working directory can be committed and pushed back to the bare repo (however files should not be updated on the live server). The second approach has the advantage that the git directory is not within the document root but this is easily solved using htaccess. Is one method objectively better than the other in terms of best practice? What other advantages and disadvantages am I missing?

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  • problems doing the Django tutorial on Dreamhost using Passengers

    - by Pietro Speroni
    I have looked and I could not find this question before, and it surprises me. I am reasonably proficient in Python, and I used Dreamhost for a number of years. Now I would like to learn Django. They are finally supporting it using Passenger. Which I do not know what is. Following the instructions on Dreamhost I installed Django. Then I started following the tutorial 01. This went well, except that I could not start the server (this in the tutorial) since the code was live on dreamhost. At the time this did not seem to make any difference. Then when I went on the second part of the tutorial I had to access the admin site. And it worked well going to myurl/admin/ , as it should. But here the problems started. According to the tutorial (here) I have to add a file in the poll application and then restart the server. But I never started the server in the first place, my code is running live on the web... but when I add a file the website the admin acts as if it does not see it. Probably dreamhost has started its own server, and I don't know how to restart it. But I assume this is going to be a common problem when you run django on dreamhost. Every time you add a file you will have to tell the server to consider it. So what should I do to let the server know about it? Thanks, Pietro

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