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  • Imputing missing data in aligned sequences

    - by Kwame Oduro
    I want a simple perl script that can help me impute missing nucleotides in aligned sequences: As an example, my old_file contains the following aligned sequences: seq1 ATGTC seq2 ATGTC seq3 ATNNC seq4 NNGTN seq5 CTCTN So I now want to infer all Ns in the file and get a new file with all the Ns inferred based on the majority nucleotide at a particular position. My new_file should look like this: seq1 ATGTC seq2 ATGTC seq3 ATGTC seq4 ATGTC seq5 CTCTC A script with usage: "impute_missing_data.pl old_file new_file" or any other approach will be helpful to me. Thank you.

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  • Creating DOM elements on the fly - check if the data is not harmful

    - by user313353
    I already posted a question closely related to the this one. I watched the Mix10 video with P. Haacked and S. Hanselman. I am building an AJAX-powered site whose input forms are created on the fly. All the code to accomplish this is done within a script tag or a javascript file. For example the following DOM elements are created when the page loads and are wrapped into an existing div defined in a view: $('#myform').append('); $('#myform').append(''); When I click the submit button I need to get the values of the input form whose id is 'Name': $("#Name").val() and then I return a Json object: { Name: name }; For this kind of scenario there is no way to use Html.Encode() or AntiXss.HtmlEncode() on the client-side. The only way to check if the input is not harmful is done on the server-side (via a service layer). This seems a limitation. All is fine if and only if a view has a set of predefined inputs. When it is time to create them on the fly, the situation is different. Have you thought of that situation guys? Thanks for the attention you have put on this. Roland Brussels, Belgium

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  • Cannot access data in a xml string

    - by Jess McKenzie
    I am trying to create an array that I can include the perent category Name and the child category Name. I can so far access the below object fine using $xml->Subcategories; but if I try my code below I get an empty array why? PHP: foreach ($catDetailsXml->Category as $value) { $categoryDetails[] = array('CategoryNumber' => $value->Number); } Structure: object(SimpleXMLElement)#13 (1) { ["Category"]=> array(5) { [0]=> object(SimpleXMLElement)#14 (4) { ["Name"]=> string(19) "Commercial Property" ["Number"]=> string(10) "0350-0100-" ["Subcategories"]=> object(SimpleXMLElement)#35 (1) { ["Category"]=> array(3) { [0]=> object(SimpleXMLElement)#36 (4) { ["Name"]=> string(9) "Car parks" ["Number"]=> string(15) "0350-0100-8946-" ["Subcategories"]=> object(SimpleXMLElement)#39 (0) { } }

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  • Calling a function that resides in the main page from a plugin?

    - by Justin Lee
    I want to call a function from within plugin, but the function is on the main page and not the plugin's .js file. EDIT I have jQuery parsing a very large XML file and building, subsequently, a large list (1.1 MB HTML file when dynamic content is copied, pasted, then saved) that has expand/collapse functionality through a plugin. The overall performance on IE is super slow and doggy, assuming since the page/DOM is so big. I am currently trying to save the collapsed content in the event.data when it is collapsed and remove it from the DOM, then bring it back when it is told to expand... the issue that I am having is that when I bring the content back, obviously the "click" and "hover" events are gone. I'm trying to re-assign them, currently doing so inside the plugin after the plugin expands the content. The issue then though is that is says the function that I declare within the .click() is not defined. Also the hover event doesn't seem to be re-assigning either.... if ($(event.data.trigger).attr('class').indexOf('collapsed') != -1 ) { // if expanding // console.log(event.data.targetContent); $(event.data.trigger).after(event.data.targetContent); $(event.data.target).hide(); /* This Line --->*/ $(event.data.target + 'a.addButton').click(addResourceToList); $(event.data.target + 'li.resource') .hover( function() { if (!($(this).attr("disabled"))) { $(this).addClass("over"); $(this).find("a").css({'display':'block'}); } }, function () { if (!($(this).attr("disabled"))) { $(this).removeClass("over"); $(this).children("a").css({'display':'none'}); } } ); $(event.data.target).css({ "height": "0px", "padding-top": "0px", "padding-bottom": "0px", "margin-top": "0px", "margin-bottom": "0px"}); $(event.data.target).show(); $(event.data.target).animate({ height: event.data.heightVal + "px", paddingTop: event.data.topPaddingVal + "px", paddingBottom: event.data.bottomPaddingVal + "px", marginTop: event.data.topMarginVal + "px", marginBottom: event.data.bottomMarginVal + "px"}, "normal");//, function(){$(this).hide();}); $(event.data.trigger).removeClass("collapsed"); $.cookies.set('jcollapserSub_' + event.data.target, 'expanded', {hoursToLive: 24 * 365}); } else if ($(event.data.trigger).attr('class').indexOf('collapsed') == -1 ) { // if collapsing $(event.data.target).animate({ height: "0px", paddingTop: "0px", paddingBottom: "0px", marginTop: "0px", marginBottom: "0px"}, "normal", function(){$(this).hide();$(this).remove();}); $(event.data.trigger).addClass("collapsed"); $.cookies.set('jcollapserSub_' + event.data.target, 'collapsed', {hoursToLive: 24 * 365}); } EDIT So, having new eyes truly makes a difference. As I was reviewing the code in this post this morning after being away over the weekend, I found where I had err'd. This: $(event.data.target + 'a.addButton').click(addResourceToList); Should be this (notice the space before a.addbutton): $(event.data.target + ' a.addButton').click(addResourceToList); Same issue with the "li.resource". So it was never pointing to the right elements... Thank you, Rene, for your help!!

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  • Why use hashing to create pathnames for large collections of files?

    - by Stephen
    Hi, I noticed a number of cases where an application or database stored collections of files/blobs using a has to determine the path and filename. I believe the intended outcome is a situation where the path never gets too deep, or the folders ever get too full - too many files (or folders) in a folder making for slower access. EDIT: Examples are often Digital libraries or repositories, though the simplest example I can think of (that can be installed in about 30s) is the Zotero document/citation database. Why do this? EDIT: thanks Mat for the answer - does this technique of using a hash to create a file path have a name? Is it a pattern? I'd like to read more, but have failed to find anything in the ACM Digital Library

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  • writing python to extract data from a file

    - by user297003
    Hi i am new to python i am trying to extract the text between that has specific text file ---- data1 data1 data1 extractme ---- data2 data2 data2 ---- data3 data3 extractme ---- and then dump it to text file so that ---- data1 data1 data1 extractme --- data3 data3 extractme --- thanks for the help data1 data1

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  • DataTriggered animation is triggered only in the first time

    - by Pavel
    I just wanted to create very simple example of DataTriggers and animation. Two checkboxes and Rectangle. Checking the first cb makes the rectangle fade away. (CodeBehind var is true) Checking the second cb makes the rectangle come back. (var is false) App is loading - the rectangle is showing (true) Firs cb is checked by default. I'm checking second cb - rect is dissapearing. It's OK. But when I then check the first cb rect isn't showing up. But checking the second cb still makes rect show up and fade away. here's my xaml and code behind: <StackPanel> <RadioButton IsChecked="True" Checked="RadioButton_Checked"></RadioButton> <RadioButton Checked="RadioButton_Checked_1"></RadioButton> <Rectangle Name="r1" Width="100" Height="300" Fill="Green"> <Rectangle.Style> <Style TargetType="Rectangle"> <Style.Triggers> <DataTrigger Binding="{Binding Active}" Value="True"> <DataTrigger.EnterActions> <BeginStoryboard> <Storyboard> <DoubleAnimation Storyboard.TargetProperty="Opacity" From="0" To="1" Duration="0:0:1" /> </Storyboard> </BeginStoryboard> </DataTrigger.EnterActions> </DataTrigger> <DataTrigger Binding="{Binding Active}" Value="False"> <DataTrigger.EnterActions> <BeginStoryboard> <Storyboard> <DoubleAnimation Storyboard.TargetProperty="Opacity" From="1" To="0" Duration="0:0:1" /> </Storyboard> </BeginStoryboard> </DataTrigger.EnterActions> </DataTrigger> </Style.Triggers> </Style> </Rectangle.Style> </Rectangle> </StackPanel> public bool Active { get { return (bool) GetValue(ActiveProperty); } set { SetValue(ActiveProperty, value); } } public static readonly DependencyProperty ActiveProperty = DependencyProperty.Register("Active", typeof(bool), typeof(MainWindow), new UIPropertyMetadata(false)); private void RadioButton_Checked(object sender, RoutedEventArgs e) { Active = true; } private void RadioButton_Checked_1(object sender, RoutedEventArgs e) { Active = false; }

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  • Rogue PropertyChanged notifications from ViewModel

    - by user1886323
    The following simple program is causing me a Databinding headache. I'm new to this which is why I suspect it has a simple answer. Basically, I have two text boxes bound to the same property myString. I have not set up the ViewModel (simply a class with one property, myString) to provide any notifications to the View for when myString is changed, so even although both text boxes operate a two way binding there should be no way that the text boxes update when myString is changed, am I right? Except... In most circumstances this is true - I use the 'change value' button at the bottom of the window to change the value of myString to whatever the user types into the adjacent text box, and the two text boxes at the top, even although they are bound to myString, do not change. Fine. However, if I edit the text in TextBox1, thus changing the value of myString (although only when the text box loses focus due to the default UpdateSourceTrigger property, see reference), TextBox2 should NOT update as it shouldn't receive any updates that myString has changed. However, as soon as TextBox1 loses focus (say click inside TextBox2) TextBox2 is updated with the new value of myString. My best guess so far is that because the TextBoxes are bound to the same property, something to do with TextBox1 updating myString gives TextBox2 a notification that it has changed. Very confusing as I haven't used INotifyPropertyChanged or anything like that. To clarify, I am not asking how to fix this. I know I could just change the binding mode to a oneway option. I am wondering if anyone can come up with an explanation for this strange behaviour? ViewModel: namespace WpfApplication1 { class ViewModel { public ViewModel() { _myString = "initial message"; } private string _myString; public string myString { get { return _myString; } set { if (_myString != value) { _myString = value; } } } } } View: <Window x:Class="WpfApplication1.MainWindow" xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation" xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" xmlns:local="clr-namespace:WpfApplication1" Title="MainWindow" Height="350" Width="525"> <Window.DataContext> <local:ViewModel /> </Window.DataContext> <Grid> <!-- The culprit text boxes --> <TextBox Height="23" HorizontalAlignment="Left" Margin="166,70,0,0" Name="textBox1" VerticalAlignment="Top" Width="120" Text="{Binding Path=myString, Mode=TwoWay}" /> <TextBox Height="23" HorizontalAlignment="Left" Margin="166,120,0,0" Name="textBox2" VerticalAlignment="Top" Width="120" Text="{Binding Path=myString, Mode=TwoWay}"/> <!--The buttons allowing manual change of myString--> <Button Name="changevaluebutton" Content="change value" Click="ButtonUpdateArtist_Click" Margin="12,245,416,43" Width="75" /> <Button Content="Show value" Height="23" HorizontalAlignment="Left" Margin="12,216,0,0" Name="showvaluebutton" VerticalAlignment="Top" Width="75" Click="showvaluebutton_Click" /> <Label Content="" Height="23" HorizontalAlignment="Left" Margin="116,216,0,0" Name="showvaluebox" VerticalAlignment="Top" Width="128" /> <TextBox Height="23" HorizontalAlignment="Left" Margin="116,245,0,0" Name="changevaluebox" VerticalAlignment="Top" Width="128" /> <!--simply some text--> <Label Content="TexBox1" Height="23" HorizontalAlignment="Left" Margin="99,70,0,0" Name="label1" VerticalAlignment="Top" Width="61" /> <Label Content="TexBox2" Height="23" HorizontalAlignment="Left" Margin="99,118,0,0" Name="label2" VerticalAlignment="Top" Width="61" /> </Grid> </Window> Code behind for view: namespace WpfApplication1 { /// <summary> /// Interaction logic for MainWindow.xaml /// </summary> public partial class MainWindow : Window { ViewModel viewModel; public MainWindow() { InitializeComponent(); viewModel = (ViewModel)this.DataContext; } private void showvaluebutton_Click(object sender, RoutedEventArgs e) { showvaluebox.Content = viewModel.myString; } private void ButtonUpdateArtist_Click(object sender, RoutedEventArgs e) { viewModel.myString = changevaluebox.Text; } } }

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  • jquery.ui.tabs.js doesn't load tab data in IE9, Chrome - works perfectly fine in firefox

    - by Salma Khan
    I have few issues that I am facing on my site and I have no idea how to fix those. Please go to http://link.zambeel.ca/index.php/component/obituary/detail/52 and click on Photos tab, it doesn't load images promptly in IE9 and Chrome. I have made it work in firefox with the following code: var loadNextTab = function() { if (indexesToLoad.length == 0) return; var index = indexesToLoad.shift(); $("#tabs-1").tabs("load",index); }; $("#tabs-1").tabs({ cache: true, load: loadNextTab }); Please help me resolve this matter as soon as possible. Just to let you guys know, I am not a programmer by any means.

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  • Having problems creating an array from XML data in Acrobat Javascript, please help if you can

    - by Kevin Minke
    I have a manually created array that already works example below: var PartsData = { 179: { ref:"", partNum: "201-2007-C00-00", descript: "System Monitor Card (Tracewell Only)", cage: "39764", qty: "1", SMR: "XBOZZ", UOC: "A" }}; Now this array above is is just one value in the array and it works fine. Here is the XML that I am trying to use to dynamically change the values. <?xml version="1.0" encoding="utf-8"?> <partsTables> <partsList> <part sheetNum="ta1"> <breakDownIndexNo>-1 </breakDownIndexNo> <referenceDesg/> <indent>20534220P01 </indent> <description/> <cage>TAC RI, GRADE-A SHOCK (TEC RACK), ALT P/N 72304-1</cage> <qtyPerAssy>23991 </qtyPerAssy> <smr>1 </smr> <uoc>ADODD </uoc> <blank/> </part> </partsList> </partsTables> I have this parsing just fine in Acrobat. Now I want to make the array work for me in using these values. if I have the following below it will work. Where part.item(i).indent.value equals the value of the indent node, etc. newArr = { 179: { ref: part.item(i).referenceDesg.value, partNum: part.item(i).indent.value, descript: part.item(i).cage.value, cage: part.item(i).qtyPerAssy.value, qty: part.item(i).smr.value, SMR: part.item(i).uoc.value, UOC: part.item(i).blank.value}}; As soon as I try to make the 179 value, which is in the breakDownIndexNo node, dynamic by using the direct part.item(i).breakDownIndexNo.value it will not compile. Acrobat is using javascript so I'm not sure why I can not get this to parse. I have tried to create a variable out of the breakDownIndexNo node and typed it to both a String and an Integer. this will let it create the array but it will not let me output from the array. newArr[indexNum].partNum gives me "no properties" where newArr[179].partNum if I were to manually set the index number to 179 will print out the value of part.item(i).indent.value. If any of you have an idea or an answer please let me know.

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  • Nested Data XML design

    - by esryl
    Looking to nest (to unlimited levels) elements in XML. Like so: <items> <item> <name>Item One</name> <item> <name>Item Two</name> </item> <item> <name>Item Three</name> <item> <name>Item Four</name> </item> <!-- etc... --> </item> </item> </items> However. While browsing for a solution I noticed in the comments of: http://stackoverflow.com/questions/988139/weird-nesting-in-xml while the above is well formed it would not validate against any sinsible DTD. Two things, what is a better way of nesting similar elements, and secondly what would be the design of the DTD. UPDATE: Would prefer to validate against an XML Schema rather than DTD.

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  • Why does dynamic array always double by a factor of 2?

    - by Phoenix
    I was wondering how does one decide the resizing factor by which dynamic array resizes ? On wikipedia and else where I have always seen the number of elements being increased by a factor of 2? Why 2? Why not 3? how does one decide this factor ? IF it is language dependent I would like to know this for Java.

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  • Pass form data from block to a page view in Drupal

    - by abdesignuk
    I am using the location module and views module for a postcode search, which works fine in a page display using views. However I want the user to be able to enter their postcode into a block on the homepage and clicking submit my module sends them to the page created in views and the postcode is set as a session S_SESSION['postcode'] before sending to this page, next I want the location page to load but using the session to display the locations automatically. Any ideas I am using hook_form_submit() and inside that declaring the $form_state as a session and then using $form_state['redirect'] to sent to the views page path.

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  • low latency data link pc to android

    - by steveh
    can anyone recommend a method for low latency bi-directional com link between my pc app and android slave app. the app i have works now via wifi but the latency is too slow (about 300mS), i'm looking to get it down to 10mS or so. the android is acting like a glorified remote control to the game on the pc. the apk displays a low res image and sends button presses back to the game and the round trip need to be quick i'm thinking the only option beside the network, is to connect a usb cable but i don't see a lot of support for that path and not even sure it would be lower latency than wifi any ideas please?

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  • How to optimize this Python code?

    - by RandomVector
    def maxVote(nLabels): count = {} maxList = [] maxCount = 0 for nLabel in nLabels: if nLabel in count: count[nLabel] += 1 else: count[nLabel] = 1 #Check if the count is max if count[nLabel] > maxCount: maxCount = count[nLabel] maxList = [nLabel,] elif count[nLabel]==maxCount: maxList.append(nLabel) return random.choice(maxList) nLabels contains a list of integers. The above function returns the integer with highest frequency, if more than one have same frequency then a randomly selected integer from them is returned. E.g. maxVote([1,3,4,5,5,5,3,12,11]) is 5

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  • using lazy C++ for stub generation

    - by Abruzzo Forte e Gentile
    Hi all Have you ever used lazy C++? I am trying to create .CPP files out of .H files. In forum I read that it is possible with your tool but I tried touse it and I didn't succeed. Can you help me? I used the option -c with a Test.h file with exactly the following declaration. class TEST_A { public: TEST_A(); ~TEST_A(); void fooA( MyNamespace::String& aName ); }; The only thing I have is a Cpp file with written #define LZZ_INLINE #undef LZZ_INLINE and the .h file modified with before the class #define LZZ_LINE inline class TEST_A { public: TEST_A(); ~TEST_A(); void fooA( MyNamespace::String& aName ); }; #undef LZZ_LINE What I am doing wrong?

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  • Access to map data

    - by herzl shemuelian
    I have a complex map that defined typedef short short1 typedef short short2 typedef map<short1,short2> data_list; typedef map<string,list> table_list; I have a class that fill table_list class GroupingClass { table_list m_table_list; string Buildkey(OD e1){ string ostring; ostring+=string(e1.m_Date,sizeof(Date)); ostring+=string(e1.m_CT,sizeof(CT)); ostring+=string(e1.m_PT,sizeof(PT)); return ostring; } void operator() (const map<short1,short2>::value_type& myPair) { OptionsDefine e1=myPair.second; string key=Buildkey(e1); m_table_list[key][e1.m_short2]=e1.m_short2; } operator table_list() { return m_table_list; } }; and I use it by table_list TL2 GroupingClass gc; TL2=for_each(mapOD.begin(), mapOD.end(), gc); but when I try to access to internal map I have problems for example data_list tmp; tmp=TL2["AAAA"]; short i=tmp[1]; //I dont update i variable but if i use a loop by itrator this work properly why this no work at first way thanks herzl

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  • [BST] Deletion procedure

    - by Metz
    Hi all. Consider the deletion procedure on a BST, when the node to delete has two children. Let's say i always replace it with the node holding the minimum key in its right subtree. The question is: is this procedure commutative? That is, deleting x and then y has the same result than deleting first y and then x? I think the answer is no, but i can't find a counterexample, nor figure out any valid reasoning. Thank you. EDIT: Maybe i've got to be clearer. Consider the transplant(node x, node y) procedure: it replace x with y (and its subtree). So, if i want to delete a node (say x) which has two children i replace it with the node holding the minimum key in its right subtree: y = minimum(x.right) transplant(y, y.right) // extracts the minimum (it doesn't have left child) y.right = x.right y.left = x.left transplant(x,y) The question was how to prove the procedure above is not commutative.

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