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  • Subprocess fails to catch the standard output

    - 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 "<string>", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in <module> 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • Finding backedges in a graph, with special conditions.

    - by Morteza M.
    There is a vertex v, such that from the subtree rooted at v, there are at least two backedges to proper ancestors of v. The problem is finding whether such backedges exist or not ( finding v is not important at all). I run DFS algorithm, I can find backedges and save them in an array. I know which backedges in this array belong to a common tree. but I have problem on matching this condition in O(E) time. can anyone help me with that?

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  • Reliable way to get the "ancestor" of an object with a specific classname, using jQuery

    - by Matt Dawdy
    I've got a javascript function that gets called on change event of a select form element. So, the "this" variable in js refers to the select element. This select element is in a td tag, in a tr tag. The tr tag has a classname of "FilterDetailsRow". Now, I've tested, and if I use this syntax: var filterRow = $(this).parent().parent(); it gets me what I want. However, is there a better way to tell jQuery, "starting with "this" can you please go up my tree of parents until you find one with a classname of "FilterDetailsRow"? Here's what I came up with, but I want to make sure I"m not reinventing the wheel. function GetFilterDetailsRowOfObject(o) { if (o) { if (o.parent()[0].className.indexOf("FilterDetailsRow") != -1) return o; else return GetFilterDetailsRowOfObject(o.parent()); } else { return null; } } Thanks for any advice.

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  • Best solution for managing navigation (and marking currently active item) in CakePHP

    - by Nathan
    So I have been looking around for a couple hours for a solid solution to handling site navigation in CakePHP. Over the course of a dozen projects, I have rigged together something that works for each one, but what I'm looking for is ideally a CakePHP plugin that handles the following: Navigation Model Component for handing off to the view Element View Helper for displaying the navigation (with control over sublevels displayed and automatically determining the "active" item based on URL and/or controller/model/slug Admin pages for managing a tree of navigation Any suggestions for an all-in-one solution or even the individual components would be very appreciated! Or even suggestions on how you have handled it in the past

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  • How to remove svn folders over FTP

    - by Loftx
    Hi there, I've accidentally copied a large part of a folder tree from my SVN working copy to my shared Windows web host via FTP. The site is now littered with .svn directories and and I need some way of cleaning them. The only access I have to the server is via FTP, or by running a script on the server. Does any one have a script which can be run remotely to remove the files over FTP (any language Windows/Linux is fine) or a script in ASP, ASP.net or PHP I can run directly on the server to remove these directories? Thanks, Tom

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  • Class 'org.springframework.http.converter.ResourceHttpMessageConverter' not found - how to correct?

    - by Ash Kim
    Eclipse STS is reporting I have problem with my spring project. It's a fresh project generated from the Spring Web MVC Project Template (File-New-Spring Template Project-Spring Web MVC ). When I create the project it has no problems - it's only once I modify the pom (by adding the hibernate dependencies) that STS then picks up the spring problem. Strangely if I revert the pom the problem remains. Also I can run the project on a spring tc server and all works correctly. Any ideas how I can satisfy this problem report? "Class 'org.springframework.http.converter.ResourceHttpMessageConverter' not found" mvc-config.xml /src/main/webapp/WEB-INF/spring line 9 Spring Beans Problem mvc-config.xml: <?xml version="1.0" encoding="UTF-8"?> <beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:mvc="http://www.springframework.org/schema/mvc" xsi:schemaLocation=" http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-3.0.xsd http://www.springframework.org/schema/mvc http://www.springframework.org/schema/mvc/spring-mvc-3.0.xsd"> <mvc:annotation-driven /> <!-- <= PROBLEMATIC LINE REPORTED BY STS --> <!-- Resolves view names to protected .jsp resources within the /WEB-INF/views directory --> <bean class="org.springframework.web.servlet.view.InternalResourceViewResolver"> <property name="prefix" value="/WEB-INF/views/"/> <property name="suffix" value=".jsp"/> </bean> </beans>

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  • How can I determine file encodings on Windows / IIS ?

    - by Dylan Beattie
    From the answers to this question it appears there's a file somewhere on our server that's been saved with the wrong encoding. I've seen this happen before - most often when pasting from Word into Visual Studio, when "smart quotes" can interfere with Visual Studio's encoding settings when saving the file. Thing is - the problem I'm having involves 20-30 different script files, include files and so on (hey, that was how we kept it modular back in the day...) and I really don't want to open every one of them in Visual Studio and check the file encodings individually. Is there any way I can analyze a folder tree full of files and spit out a list of each filename along with the text encoding used to save the file? (Or - if encodings aren't clearly specified - work out what encoding Microsoft IIS thinks was used to save the file?)

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  • UI form component for ASP NET MVC

    - by Bugeo
    Hi I'd like to find a component that help me to build input forms in asp MVC. I find that ther are many components (grid, tree, tab...) but not a "Form component". I know that i can use the HTML HELPER (.labelfor(.. .inputTextFor(... ) ..but i don't like to write the html tags around the fields and labels ( ... ) I want that all the form in my application look similar and, if a change is needed i want to make it in one place ( ex in the "FormComponentFactory()" for example ) I created my own FormComponent but i find myself reinvent the wheel..

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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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  • Write directly to a remote Git repository, without adding objects to a local index/repo?

    - by Ryan B. Lynch
    Does Git support any commands that would allow me to commit directly from a local/working tree into a remote repository? The normal workflow requires a "git add", at least, to populate the object database with copies of the file contents, etc. I understand that this is NOT the normal, expected Git workflow. But I noticed that Git already supports downloading directly from the repository, with no local repo ("git archive"), so it seems reasonable that there might be a similar uploading operation. Alternatively, if there isn't such a command in the core Git itself, does any 3rd-party software support direct remote writes?

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  • how to register a selectionProvider for the Viewer from a superclass

    - by Tom
    I have a View which extends a View provided by another plugin like this; public class View2 extends some.other.package.View1 { public void createPartControl(Composite parent) { super.createPartControl(parent); //I want to do this, but I can't because its private //getSite().setSelectionProvider(treeViewer); } } But I can't edit the super class, so I need to access the viewer from the Control. public class some.other.package.View1 extends ViewPart { private TreeViewer treeViewer; public void createPartControl(Composite parent) { treeViewer = new TreeViewer(parent, SWT.V_SCROLL); } } I tried using parent.getChildren(); to get a Tree object, but I can't see that it can be cooerced into an ISElectionProvider as required

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  • Save PyML.classifiers.multi.OneAgainstRest(SVM()) object?

    - by Michael Aaron Safyan
    I'm using PYML to construct a multiclass linear support vector machine (SVM). After training the SVM, I would like to be able to save the classifier, so that on subsequent runs I can use the classifier right away without retraining. Unfortunately, the .save() function is not implemented for that classifier, and attempting to pickle it (both with standard pickle and cPickle) yield the following error message: pickle.PicklingError: Can't pickle : it's not found as __builtin__.PySwigObject Does anyone know of a way around this or of an alternative library without this problem? Thanks. Edit/Update I am now training and attempting to save the classifier with the following code: mc = multi.OneAgainstRest(SVM()); mc.train(dataset_pyml,saveSpace=False); for i, classifier in enumerate(mc.classifiers): filename=os.path.join(prefix,labels[i]+".svm"); classifier.save(filename); Notice that I am now saving with the PyML save mechanism rather than with pickling, and that I have passed "saveSpace=False" to the training function. However, I am still gettting an error: ValueError: in order to save a dataset you need to train as: s.train(data, saveSpace = False) However, I am passing saveSpace=False... so, how do I save the classifier(s)? P.S. The project I am using this in is pyimgattr, in case you would like a complete testable example... the program is run with "./pyimgattr.py train"... that will get you this error. Also, a note on version information: [michaelsafyan@codemage /Volumes/Storage/classes/cse559/pyimgattr]$ python Python 2.6.1 (r261:67515, Feb 11 2010, 00:51:29) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright", "credits" or "license" for more information. import PyML print PyML.__version__ 0.7.0

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  • Managing Strategy objects with Hibernate & Spring

    - by Francois
    This is a design question better explained with a Stack Overflow analogy: Users can earn Badges. Users, Badges and Earned Badges are stored in the database. A Badge’s logic is run by a Badge Condition Strategy. I would prefer not to have to store Badge Condition Strategies in the database, because they are complex tree structure objects. How do I associate a Badge stored in the database with its Badge Condition Strategy? I can only think of workaround solutions. For example: create 1 class per badge and use a SINGLE_TABLE inheritance strategy. Or get the badge from the database, and then programmatically lookup and inject the correct Badge Condition Strategy. Thanks for suggesting a better design.

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  • Creating a "netbeans property" style dialog box

    - by pikco
    Hi I've been trying to create a GUI using netbeans, that includes a dialog similar to Netbean's own "property dialog" that appears when designing. ie. a dialog that contains a table that can be expanded by tree nodes. Something like the dialog on this page, http://platform.netbeans.org/tutorials/nbm-property-editors.html As far as I can understand, the page I linked to describes a custom editor I can set up for use within netbeans while designing - I'm just looking for a way to doing something similar for my actual application I'm writing. Is there an easy way to do this? I came across this and have tried it but it doesn't quite work in the same way as the standard Netbeans dialog. weblogs.java.net/blog/timboudreau/archive/2008/06/egads_an_actual.html Any tips greatly appreciated.

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  • Java Heap Overflow, Forcing Garbage Collection

    - by Nicholas
    I've create a trie tree with an array of children. When deleting a word, I set the children null, which I would assume deletes the node(delete is a relative term). I know that null doesn't delete the child, just sets it to null, which when using a large amount of words it causes to overflow the heap. Running a top on linux, I can see my memory usage spike to 1gb pretty quickly, but if I force garbage collection after the delete (Runtime.gc()) the memory usage goes to 50mb and never above that. From what I'm told, java by default runs garbage collection before a heap overflow happens, but I can't see to make that happen.

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  • Error while updating Database record with Entity Framework on ASP.NET MVC Page

    - by Rupa
    Hi I have an ASP.NET Page that updates registered User Address Details for a selected record. Below is the Update method that i am calling from Controller. When i am calling ApplyPropertyChanges method, I am getting the below error. Did anyone run into the same error while updating the record with Entity Framework. Appreciate your responses. Error Message: The existing object in the ObjectContext is in the Added state. Changes can only be applied when the existing object is in an unchanged or modified state. My Update Method Code: [HttpPost] public bool UpdateAddressDetail([Bind(Prefix = "RegUser")] AddressDetail regUserAddress, FormCollection formData) { regUserAddress.AD_Id = 3; regUserAddress.LastUpdated = HttpContext.User.Identity.Name; regUserAddress.UpdatedOn = DateTime.Now; regUserAddress.AddressType = ((AddressDetail)Session["CurrentAddress"]).AddressType ?? "Primary"; regUserAddress.Phone = ((AddressDetail)Session["CurrentAddress"]).Phone; regUserAddress.Country = ((AddressDetail)Session["CurrentAddress"]).AddressType ?? "USA"; miEntity.ApplyPropertyChanges(regUserAddress.EntityKey.EntitySetName, regUserAddress); miEntity.SaveChanges(); return true; }

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  • java Getting a list of words from a Trie

    - by adam08
    I'm looking to use the following code to not check whether there is a word matching in the Trie but to return a list all words beginning with the prefix inputted by the user. Can someone point me in the right direction? I can't get it working at all..... public boolean search(String s) { Node current = root; System.out.println("\nSearching for string: "+s); while(current != null) { for(int i=0;i<s.length();i++) { if(current.child[(int)(s.charAt(i)-'a')] == null) { System.out.println("Cannot find string: "+s); return false; } else { current = current.child[(int)(s.charAt(i)-'a')]; System.out.println("Found character: "+ current.content); } } // If we are here, the string exists. // But to ensure unwanted substrings are not found: if (current.marker == true) { System.out.println("Found string: "+s); return true; } else { System.out.println("Cannot find string: "+s +"(only present as a substring)"); return false; } } return false; } }

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  • java.lang.ClassNotFoundException: org.springframework.ui.ModelMap

    - by aelshereay
    I create a simple webapp using tomcat 6, spring 2.5.6 and maven. The problem is when I boot up tomcat, I am getting the following errors: SEVERE: StandardWrapper.Throwable java.lang.NoClassDefFoundError: org/springframework/ui/ModelMap ... Caused by: java.lang.ClassNotFoundException: org.springframework.ui.ModelMap The ModelMap class does exist in spring-2.5.6.jar and spring-context-2.5.6.jar, I also have some other spring jars. All of them are being deployed to tomcat correctly, when I check the application WEB-INF (deployed to tomcat) I found all those jars there! I have only one @Controller that has a @RequestMapping("/home.htm") showForm(ModelMap model) method. My applicationContext is quite simple: <?xml version="1.0" encoding="utf-8"?> <beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop" xmlns:context="http://www.springframework.org/schema/context" xmlns:dwr="http://www.directwebremoting.org/schema/spring-dwr" xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-2.5.xsd http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-2.5.xsd http://www.directwebremoting.org/schema/spring-dwr http://www.directwebremoting.org/schema/spring-dwr-3.0.xsd" default-autowire="byName"> <context:component-scan base-package="org.myapp"/> <bean class="org.springframework.web.servlet.mvc.annotation.DefaultAnnotationHandlerMapping"/> <bean class="org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter"/> <bean id="viewResolver" class="org.springframework.web.servlet.view.InternalResourceViewResolver"> <property name="viewClass" value="org.springframework.web.servlet.view.JstlView"></property> <property name="prefix" value="/WEB-INF/view/"></property> <property name="suffix" value=".jsp"></property> </bean> </beans>

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  • ModelState always valid

    - by Jaimal Chohan
    I've got something seemingly very simple not working. I have got a model public class Name: Entity { [StringLength(10), Required] public virtual string Title { get; set; } } public class Customer: Entity { public virtual Name Name { get; set; } } a view model public class CustomerViweModel { public Customer Customer { get; set; } } a view <% using(Html.BeginForm()) { %> <%= Html.LabelFor(m => m.Customer.Name.Title)%> <button type="submit">Submit</button> <% } %> and a controller [HttpPost] public ActionResult Index([Bind(Prefix = "Customer")] Customer customer) { if(ModelState.IsValid) Save else return View(); } No matter what I enter as the title (null, or a string 10 chars), ModelState.IsValid is always true. The Title field in the Customer object has a value, so the data is being passed around, but not being validated? Any clues?

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