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

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

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  • Suppress the HTTP_X_FORWARDED_FOR http header, c# .net C++

    - by Sean
    I'm writing an application in C# that uses proxies. The proxies are sending the HTTP_X_FORWARDED_FOR during HTTP requests, and this is unwanted behavior. I am extending the Interop.SHDocVw axWebBrowser (aka Internet Explorer) control right now, but can take another approach if needed for this problem. Is there some way to suppress this header... can this be done in code, on the proxy server, or not at all?

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  • Jquery and Hide a div on a click

    - by hann
    hello, i have a little problem with JQuery. Well, i have a and i want to hide this div when an user click in a zone that is not in the like the "notifications" behavior in facebook. The solution that i found is to use jQuery.live() method but i think there is a better way to do it. Thank you.

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  • factory girl - know when an attribute is overridden in factory

    - by carlos
    Is there any way to determine if attributes are overridden in a factory and adjust the behavior of the factory based on those overrides? The evaluator passed into the callbacks contains a __override_names__ method. Unfortunately, by the time it is passed to the callback, every attribute configured by the factory is included in the array returned. Moreover, the Evaluator is marked as api private.

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  • VBA Access Import Specification strange error

    - by captonssj
    I am trying to import a text file into Access using a saved "Import Specification" in my access database using VBA. The import generates the Import Error table showing the errors in the last two fields. BUT if I use the same import specification manually to import the text file, the Import works perfect !!!!! Strange ..... why would they have different behavior ? Here is the database and the text file http://www.box.net/shared/ro7n3b7a77

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  • need a project design tool

    - by santosh
    I am looking for simple and easy to use tools through which I can get project's visual picture of folder/file tree stucture , its classes, functions and objects, relations between classes and files.

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  • Multiple instances of this carousel on a single page - can't get it to work

    - by Andy
    This code comes from a tutorial so it's not originally my own work. What I am trying to do is implement this several times on a single page. I have tried and so far failed - by numbering the id "carousel" and so forth. Any help would be seriously appreciated. I'm tearing my hair out. http://jsfiddle.net/AndyMP/zcKDV/5/ For completeness.. this is the carousel JQuery as it stands. //rotation speed and timer var speed = 5000; var run = setInterval('rotate()', speed); //grab the width and calculate left value var item_width = $('#slides li').outerWidth(); var left_value = item_width * (-1); //move the last item before first item, just in case user click prev button $('#slides li:first').before($('#slides li:last')); //set the default item to the correct position $('#slides ul').css({'left' : left_value}); //if user clicked on prev button $('#prev').click(function() { //get the right position var left_indent = parseInt($('#slides ul').css('left')) + item_width; //slide the item $('#slides ul').animate({'left' : left_indent}, 200,function(){ //move the last item and put it as first item $('#slides li:first').before($('#slides li:last')); //set the default item to correct position $('#slides ul').css({'left' : left_value}); }); //cancel the link behavior return false; }); //if user clicked on next button $('#next').click(function() { //get the right position var left_indent = parseInt($('#slides ul').css('left')) - item_width; //slide the item $('#slides ul').animate({'left' : left_indent}, 200, function () { //move the first item and put it as last item $('#slides li:last').after($('#slides li:first')); //set the default item to correct position $('#slides ul').css({'left' : left_value}); }); //cancel the link behavior return false; }); //if mouse hover, pause the auto rotation, otherwise rotate it $('#slides').hover( function() { clearInterval(run); }, function() { run = setInterval('rotate()', speed); } ); //a simple function to click next link //a timer will call this function, and the rotation will begin :) function rotate() { $('#next').click(); }

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  • Skip Lists -- ever used them?

    - by Head Geek
    I'm wondering whether anyone here has ever used a skip list. It looks to have roughly the same advantages as a balanced binary tree, but is simpler to implement. If you have, did you write your own, or use a pre-written library (and if so, what was its name)?

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  • PHP 5.3: Late static binding doesn't work for properties when defined in parent class while missing in child class

    - by DavidPesta
    Take a look at this example, and notice the outputs indicated. <?php class Mommy { protected static $_data = "Mommy Data"; public static function init( $data ) { static::$_data = $data; } public static function showData() { echo static::$_data . "<br>"; } } class Brother extends Mommy { } class Sister extends Mommy { } Brother::init( "Brother Data" ); Sister::init( "Sister Data" ); Brother::showData(); // Outputs: Sister Data Sister::showData(); // Outputs: Sister Data ?> My understanding was that using the static keyword would refer to the child class, but apparently it magically applies to the parent class whenever it is missing from the child class. (This is kind of a dangerous behavior for PHP, more on that explained below.) I have the following two things in mind for why I want to do this: I don't want the redundancy of defining all of the properties in all of the child classes. I want properties to be defined as defaults in the parent class and I want the child class definition to be able to override these properties wherever needed. The child class needs to exclude properties whenever the defaults are intended, which is why I don't define the properties in the child classes in the above example. However, if we are wanting to override a property at runtime (via the init method), it will override it for the parent class! From that point forward, child classes initialized earlier (as in the case of Brother) unexpectedly change on you. Apparently this is a result of child classes not having their own copy of the static property whenever it isn't explicitly defined inside of the child class--but instead of throwing an error it switches behavior of static to access the parent. Therefore, is there some way that the parent class could dynamically create a property that belongs to the child class without it appearing inside of the child class definition? That way the child class could have its own copy of the static property and the static keyword can refer to it properly, and it can be written to take into account parent property defaults. Or is there some other solution, good, bad, or ugly?

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  • COM library for Explorer-like system views

    - by chrisd
    To provide a Windows Explorer-like view of the user's system, we have been using the shell controls from LogicNP (formerly Sky Software), but these have deficiencies, e.g., no support for Win7 libraries. The vendor has not responded to our inquiries about updates, so we're looking to replace the package. Requirements: ActiveX (no managed code or MFC) Tree and list views of the system Per-item checkboxes 32- and 64-bit versions Any recommendations for a replacement product? TIA.

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  • Stored procedure performance randomly plummets; trivial ALTER fixes it. Why?

    - by gWiz
    I have a couple of stored procedures on SQL Server 2005 that I've noticed will suddenly take a significantly long time to complete when invoked from my ASP.NET MVC app running in an IIS6 web farm of four servers. Normal, expected completion time is less than a second; unexpected anomalous completion time is 25-45 seconds. The problem doesn't seem to ever correct itself. However, if I ALTER the stored procedure (even if I don't change anything in the procedure, except to perhaps add a space to the script created by SSMS Modify command), the completion time reverts to expected completion time. IIS and SQL Server are running on separate boxes, both running Windows Server 2003 R2 Enterprise Edition. SQL Server is Standard Edition. All machines have dual Xeon E5450 3GHz CPUs and 4GB RAM. SQL Server is accessed using its TCP/IP protocol over gigabit ethernet (not sure what physical medium). The problem is present from all web servers in the web farm. When I invoke the procedure from a query window in SSMS on my development machine, the procedure completes in normal time. This is strange because I was under the impression that SSMS used the same SqlClient driver as in .NET. When I point my development instance of the web app to the production database, I again get the anomalous long completion time. If my SqlCommand Timeout is too short, I get System.Data.SqlClient.SqlException: Timeout expired. The timeout period elapsed prior to completion of the operation or the server is not responding. Question: Why would performing ALTER on the stored procedure, without actually changing anything in it, restore the completion time to less than a second, as expected? Edit: To clarify, when the procedure is running slow for the app, it simultaneously runs fine in SSMS with the same parameters. The only difference I can discern is login credentials (next time I notice the behavior, I'll be checking from SSMS with the same creds). The ultimate goal is to get the procs to sustainably run with expected speed without requiring occasional intervention. Resolution: I wanted to to update this question in case others are experiencing this issue. Following the leads of the answers below, I was able to consistently reproduce this behavior. In order to test, I utilize sp_recompile and pass it one of the susceptible sprocs. I then initiate a website request from my browser that will invoke the sproc with atypical parameters. Lastly, I initiate a website request to a page that invokes the sproc with typical parameters, and observe that the request does not complete because of a SQL timeout on the sproc invocation. To resolve this on SQL Server 2005, I've added OPTIMIZE FOR hints to my SELECT. The sprocs that were vulnerable all have the "all-in-one" pattern described in this article. This pattern is certainly not ideal but was a necessary trade-off given the timeframe for the project.

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  • Are IIS services closed after some time?

    - by mafutrct
    I'd like to host a WCF web service in IIS. The service should keep a certain set of data all the time, it must never be lost. My colleague told me this is impossible because IIS closes down the service after a certain time (I assume without any activity). Is that true? How do I prevent that behavior? In case it matters, both IIS 6 and 7 are available.

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  • Visual Studio Question: How to go to a specific file path and line number programmatically?

    - by Jack
    In the Visual Studio output window, you can double click a line that contains a file path and line number and it automatically takes you to that location. In my program, I need to mimic this behavior and be able to click something (a button for example) and do go to a specific file and line number that I tell it to go to. Any help/suggestions would be appreciated. I am working in C#.

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  • How to manipulate file paths intelligently in .Net 3.0?

    - by Hamish Grubijan
    Scenario: I am maintaining a function which helps with an install - copies files from PathPart1/pending_install/PathPart2/fileName to PathPart1/PathPart2/fileName. It seems that String.Replace() and Path.Combine() do not play well together. The code is below. I added this section: // The behavior of Path.Combine is weird. See: // http://stackoverflow.com/questions/53102/why-does-path-combine-not-properly-concatenate-filenames-that-start-with-path-dir while (strDestFile.StartsWith(@"\")) { strDestFile = strDestFile.Substring(1); // Remove any leading backslashes } Debug.Assert(!Path.IsPathRooted(strDestFile), "This will make the Path.Combine(,) fail)."); in order to take care of a bug (code is sensitive to a constant @"pending_install\" vs @"pending_install" which I did not like and changed (long story, but there was a good opportunity for constant reuse). Now the whole function: //You want to uncompress only the files downloaded. Not every file in the dest directory. private void UncompressFiles() { string strSrcDir = _application.Client.TempDir; ArrayList arrFiles = new ArrayList(); GetAllCompressedFiles(ref arrFiles, strSrcDir); IEnumerator enumer = arrFiles.GetEnumerator(); while (enumer.MoveNext()) { string strDestFile = enumer.Current.ToString().Replace(_application.Client.TempDir, String.Empty); // The behavior of Path.Combine is weird. See: // http://stackoverflow.com/questions/53102/why-does-path-combine-not-properly-concatenate-filenames-that-start-with-path-dir while (strDestFile.StartsWith(@"\")) { strDestFile = strDestFile.Substring(1); // Remove any leading backslashes } Debug.Assert(!Path.IsPathRooted(strDestFile), "This will make the Path.Combine(,) fail)."); strDestFile = Path.Combine(_application.Client.BaseDir, strDestFile); strDestFile = strDestFile.Replace(Path.GetExtension(strDestFile), String.Empty); ZSharpLib.ZipExtractor.ExtractZip(enumer.Current.ToString(), strDestFile); FileUtility.DeleteFile(enumer.Current.ToString()); } } Please do not laugh at the use of ArrayList and the way it is being iterated - it was pioneered by a C++ coder during a .Net 1.1 era. I will change it. What I am interested in: what is a better way of replacing PathPart1/pending_install/PathPart2/fileName with PathPart1/PathPart2/fileName within the current code. Note that _application.Client.TempDir is just _application.Client.BaseDir + @"\pending_install". While there are many ways to improve the code, I am mainly concerned with the part which has to do with String.Replace(...) and Path.Combine(,). I do not want to make changes outside of this function. I wish Path.Combine(,) took an optional bool flag, but it does not. So ... given my constraints, how can I rework this so that it starts to sucks less? Thanks!

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  • What to Expect in Rails 4

    - by mikhailov
    Rails 4 is nearly there, we should be ready before it released. Most developers are trying hard to keep their application on the edge. Must see resources: 1) @sikachu talk: What to Expect in Rails 4.0 - YouTube 2) Rails Guides release notes: http://edgeguides.rubyonrails.org/4_0_release_notes.html There is a mix of all major changes down here: ActionMailer changes excerpt: Asynchronously send messages via the Rails Raise an ActionView::MissingTemplate exception when no implicit template could be found ActionPack changes excerpt Added controller-level etag additions that will be part of the action etag computation Add automatic template digests to all CacheHelper#cache calls (originally spiked in the cache_digests plugin) Add Routing Concerns to declare common routes that can be reused inside others resources and routes Added ActionController::Live. Mix it in to your controller and you can stream data to the client live truncate now always returns an escaped HTML-safe string. The option :escape can be used as false to not escape the result Added ActionDispatch::SSL middleware that when included force all the requests to be under HTTPS protocol ActiveModel changes excerpt AM::Validation#validates ability to pass custom exception to :strict option Changed `AM::Serializers::JSON.include_root_in_json' default value to false. Now, AM Serializers and AR objects have the same default behaviour Added ActiveModel::Model, a mixin to make Ruby objects work with AP out of box Trim down Active Model API by removing valid? and errors.full_messages ActiveRecord changes excerpt Use native mysqldump command instead of structure_dump method when dumping the database structure to a sql file. Attribute predicate methods, such as article.title?, will now raise ActiveModel::MissingAttributeError if the attribute being queried for truthiness was not read from the database, instead of just returning false ActiveRecord::SessionStore has been extracted from Active Record as activerecord-session_store gem. Please read the README.md file on the gem for the usage Fix reset_counters when there are multiple belongs_to association with the same foreign key and one of them have a counter cache Raise ArgumentError if list of attributes to change is empty in update_all Add Relation#load. This method explicitly loads the records and then returns self Deprecated most of the 'dynamic finder' methods. All dynamic methods except for find_by_... and find_by_...! are deprecated Added ability to ActiveRecord::Relation#from to accept other ActiveRecord::Relation objects Remove IdentityMap ActiveSupport changes excerpt ERB::Util.html_escape now escapes single quotes ActiveSupport::Callbacks: deprecate monkey patch of object callbacks Replace deprecated memcache-client gem with dalli in ActiveSupport::Cache::MemCacheStore Object#try will now return nil instead of raise a NoMethodError if the receiving object does not implement the method, but you can still get the old behavior by using the new Object#try! Object#try can't call private methods Add ActiveSupport::Deprecations.behavior = :silence to completely ignore Rails runtime deprecations What are the most important changes for you?

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  • How to unit test private methods in BDD / TDD?

    - by robert_d
    I am trying to program according to Behavior Driven Development, which states that no line of code should be written without writing failing unit test first. My question is, how to use BDD with private methods? How can I unit test private methods? Is there better solution than: - making private methods public first and then making them private when I write public method that uses those private methods; or - in C# making all private methods internal and using InternalsVisibleTo attribute. Robert

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  • OpenGL: Implementing transformation matrix stack

    - by Jakub M.
    In a newer OpenGL there is no matrix stack. I am working on a simple display engine, and I am going to implement the transformation stack. What is a common strategy here? Should I build a push/pop stack, and use it with a tree representing my model? I suppose this is the "old" approach, that was deprecated in the newer OpenGL versions. Maybe then it is not the best solution (it was removed for some reason)

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  • Persistent connections with pipelining

    - by Summer_More_More_Tea
    Hi: I have a question about the behavior of a browser( especially Firefox ) tackling with persistent connections: Must all the requests sent in one pipelined persistent connection direct to the same server? What about a request specified by user from address bar -- may it reuse an already established persistent connection to send its request or need another connection? Regards.

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