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  • 50 sequences in one line

    - by user343934
    I have Muttiple sequence alignment (clustal) file and i want to read this file and arrange sequences in a such a way that in looks more clear and precise in order. I am doing this from biopython using AlignIO object. My codes like this alignment = AlignIO.read("opuntia.aln", "clustal") print "Number of rows: %i" % len(align) for record in alignment: print "%s - %s" % (record.id, record.seq) My Output-- http://i48.tinypic.com/ae48ew.jpg , it looks messy and long scrolling. What i want to do is print only 50 sequences in each line and continue till the end of alignment file. I wish to have output like this---http://i45.tinypic.com/4vh5rc.jpg from --http://www.ebi.ac.uk/Tools/clustalw2/, sorry two links are just a text due to my reputation. Any suggestions, algorithm and sample code is appreciated Thanks in advance Br,

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  • Separate specific #ifdef branches

    - by detly
    In short: I want to generate two different source trees from the current one, based only on one preprocessor macro being defined and another being undefined, with no other changes to the source. If you are interested, here is my story... In the beginning, my code was clean. Then we made a new product, and yea, it was better. But the code saw only the same peripheral devices, so we could keep the same code. Well, almost. There was one little condition that needed to be changed, so I added: #if defined(PRODUCT_A) condition = checkCat(); #elif defined(PRODUCT_B) condition = checkCat() && checkHat(); #endif ...to one and only one source file. In the general all-source-files-include-this header file, I had: #if !(defined(PRODUCT_A)||defined(PRODUCT_B)) #error "Don't make me replace you with a small shell script. RTFM." #endif ...so that people couldn't compile it unless they explicitly defined a product type. All was well. Oh... except that modifications were made, components changed, and since the new hardware worked better we could significantly re-write the control systems. Now when I look upon the face of the code, there are more than 60 separate areas delineated by either: #ifdef PRODUCT_A ... #else ... #endif ...or the same, but for PRODUCT_B. Or even: #if defined(PRODUCT_A) ... #elif defined(PRODUCT_B) ... #endif And of course, sometimes sanity took a longer holiday and: #ifdef PRODUCT_A ... #endif #ifdef PRODUCT_B ... #endif These conditions wrap anywhere from one to two hundred lines (you'd think that the last one could be done by switching header files, but the function names need to be the same). This is insane. I would be better off maintaining two separate product-based branches in the source repo and porting any common changes. I realise this now. Is there something that can generate the two different source trees I need, based only on PRODUCT_A being defined and PRODUCT_B being undefined (and vice-versa), without touching anything else (ie. no header inclusion, no macro expansion, etc)?

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  • Read Values from xml file

    - by Nimesh
    I have a function TRANSLATE which reads value from the xml file based on a key. I wanna put "http://www.google.com?search=" in the xml file and read it based on the key(SEARCHER) I am confused in framing the link when it comes in Response.Write <%Dim SearchQuery1 SearchQuery1="New" Dim SearchQuery2 SearchQuery2=30 Response.Write("<A HREF=""http://www.google.com?search="&SearchQuery1&"-"&SearchQuery2&""" TARGET=""links"">http://www.google.com?search="&SearchQuery1&"-"&SearchQuery2&"</A>") %> I was trying something like this Response.Write("<A HREF=""Translate("SEARCHER")"&SearchQuery1&"-"&SearchQuery2&""" TARGET=""links"">Translate("SEARCHER")"&SearchQuery1&"-"&SearchQuery2&"</A>") but is throwing some error: Expected)' PLs let me know how can i solve this????

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  • Should I use .pl or .cgi for Perl web script files?

    - by Nano HE
    HI. I created two files 'hello.pl' and 'hello.cgi' with the code below. #!/usr/bin/perl print "Content-type:text/html\n\n"; print "hello world"; I can view the page via both http://www.mydomain.com/cgi-bin/hello.pl and http://www.mydomain.com/cgi-bin/hello.cgi. Which one is more sense in Perl web dev? BTW, the directory of 'cgi-bin' created by my VPS server, Do I need contact with my VPS support to remove it or just remain it like this URL style? Maybe http://www.mydomain.com/perDev/hello.cgi is better?

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  • Servicestack CorsFeature Global Options Handler Not Firing on Certain Routes;

    - by gizmoboy
    I've got a service setup using the CorsFeature, and am using the approach that mythz suggested in other answers, collected in a function used in the appHost file: private void ConfigureCors(Funq.Container container) { Plugins.Add(new CorsFeature(allowedOrigins: "*", allowedMethods: "GET, POST, PUT, DELETE, OPTIONS", allowedHeaders: "Content-Type, Authorization, Accept", allowCredentials: true)); PreRequestFilters.Add((httpReq, httpRes) => { //Handles Request and closes Responses after emitting global HTTP Headers if (httpReq.HttpMethod == "OPTIONS") { httpRes.EndRequest(); } }); } However, the pre-request filter is only firing on some of the service requests. One of the base entities we have in the service is a question entity, and there are custom routes defined as follows: [Route("/question")] [Route("/question/{ReviewQuestionId}", "GET,DELETE")] [Route("/question/{ReviewQuestionId}/{ReviewSectionId}", "GET")] Using POSTMAN to fire test queries (all using the OPTIONS verb), we can see that this will fire the pre-request filter: http://localhost/myservice/api/question/ But this will not: http://localhost/myservice/api/question/66 Presumably, this is because the second and third routes explicitly defined the verbs they accept, and OPTIONS isn't one of them. Is it really necessary to spell out OPTIONS in every defined route that restricts the verbs supported?

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  • xs:choice unbounded list

    - by Matt
    I want to define an XSD schema for an XML document, example below: <?xml version="1.0" encoding="utf-8"?> <view xmlns="http://localhost/model_data" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://localhost/model_data XMLSchemaView.xsd" path="wibble" id="wibble"> <text name="PageTitle">Homepage</text> <text name="Keywords">home foo bar</text> <image name="MainImage"> <description>lolem ipsum</description> <title>i haz it</title> <url>/images/main-image.jpg</url> <type>image/jpeg</type> <alt>alt text for image</alt> <width>400</width> <height>300</height> </image> <link name="TermsAndConditionsLink"> <url>/tnc.html</url> <title>Terms and Conditions</title> <target>_blank</target> </link> </view> There's a view root element and then an unknown number of field elements (of various types). I'm using the following XSD schema: <?xml version="1.0" encoding="utf-8"?> <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://localhost/model_data" targetNamespace="http://localhost/model_data" id="XMLSchema1"> <xs:element name="text" type="text_field"/> <xs:element name="view" type="model_data"/> <xs:complexType name="model_data"> <xs:choice maxOccurs="unbounded"> <xs:element name="text" type="text_field"/> <xs:element name="image" type="image_field"/> <xs:element name="link" type="link_field"/> </xs:choice> <xs:attribute name="path" type="xs:string"/> <xs:attribute name="id" type="xs:string"/> </xs:complexType> <xs:complexType name="image_field"> <xs:all> <xs:element name="description" type="xs:string"/> <xs:element name="title" type="xs:string"/> <xs:element name="type" type="xs:string"/> <xs:element name="url" type="xs:string"/> <xs:element name="alt" type="xs:string"/> <xs:element name="height" type="xs:int"/> <xs:element name="width" type="xs:int"/> </xs:all> <xs:attribute name="name" type="xs:string"/> </xs:complexType> <xs:complexType name="text_field"> <xs:simpleContent> <xs:extension base="xs:string"> <xs:attribute name="name" type="xs:string"/> </xs:extension> </xs:simpleContent> </xs:complexType> <xs:complexType name="link_field"> <xs:all> <xs:element name="target" type="xs:string"/> <xs:element name="title" type="xs:string"/> <xs:element name="url" type="xs:string"/> </xs:all> <xs:attribute name="name" type="xs:string"/> </xs:complexType> </xs:schema> This looks like it should work to me, but it doesn't and I always get the following error: Element <text> is not allowed under element <view>. Reason: The following elements are expected at this location (see below) <text> <image> <link> Error location: view / text Details cvc-model-group: Element <text> unexpected by type 'model_data' of element <view>. cvc-elt.5.2.1: The element <view> is not valid with respect to the actual type definition 'model_data'. I've never really used XSD schemas before, so I'd really appreciate it if someone could point out where I'm going wrong.

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  • Parsing html for domain links

    - by Hallik
    I have a script that parses an html page for all the links within it. I am getting all of them fine, but I have a list of domains I want to compare it against. So a sample list contains list=['www.domain.com', 'sub.domain.com'] But I may have a list of links that look like http://domain.com http://sub.domain.com/some/other/page I can strip off the http:// just fine, but in the two example links I just posted, they both should match. The first I would like to match against the www.domain.com, and the second, I would like to match against the subdomain in the list. Right now I am using url2lib for parsing the html. What are my options in completely this task?

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  • .htaccess redirect domain alias / parked domain

    - by Calua
    Hi... I have a .htaccess related question. For example, if I have two domain, a.com and b.com. All referring to one host (b.com is domain alias of a.com). I want visitor that visit a.com will be referred to url with www (http://www.a.com). As for the visitor of http://b.com will be referred to the www url (http://www.b.com). How can I do this with .htaccess?? Thanks, any help will be much appreciated :)

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  • Htaccess strange behaviour with Nginx

    - by Termos
    I have a site running on Nginx (v1.0.14) serving as reverse proxy which proxies requests to Apache (v2.2.19). So Nginx runs on port 80, Apache is on 8080. Overall site works fine except that i cannot block access to certain directories with .htaccess file. For example i have 'my-protected-directory' on 'www.site.com' Inside it i have htaccess with following code: <Files *> order deny,allow deny from all allow from 1.2.3.4 <--- my ip address here </Files> When i try to access this page with my ip (1.2.3.4) i get 404 error which is not what i expect: http://www.site.com/my-protected-directory However everything works as expected when this page is served directly by Apache. I can see this page, everyone else can't. http://www.site.com:8080/my-protected-directory Update. Nginx config (7.1.3.7 is site ip.): user apache; worker_processes 4; error_log logs/error.log; pid logs/nginx.pid; events { worker_connections 1024; } http { include mime.types; default_type application/octet-stream; log_format main '$remote_addr - $remote_user [$time_local] "$request" ' '$status $body_bytes_sent "$http_referer" ' '"$http_user_agent" "$http_x_forwarded_for"'; sendfile on; keepalive_timeout 65; gzip on; gzip_min_length 1024; gzip_http_version 1.1; gzip_proxied any; gzip_comp_level 5; gzip_types text/plain text/css application/x-javascript text/xml application/xml application/xml+rss text/javascript image/x-icon; server { listen 80; server_name www.site.com site.com 7.1.3.7; access_log logs/host.access.log main; # serve static files location ~* ^.+.(jpg|jpeg|gif|png|ico|css|zip|tgz|gz|rar|bz2|doc|xls|exe|pdf|ppt|txt|tar|mid|midi|wav|bmp|rtf|js)$ { root /var/www/vhosts/www.site.com/httpdocs; proxy_set_header Range ""; expires 30d; } # pass requests for dynamic content to Apache location / { proxy_redirect off; proxy_set_header X-Real-IP $remote_addr; proxy_set_header Host $http_host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; proxy_set_header Range ""; proxy_pass http://7.1.3.7:8080; } } Could please anyone tell me what is wrong and how this can be fixed ?

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  • Favicon to PNG in PHP

    - by sailtheworld
    I need a PHP script to convert favicons to PNGs while keeping their original dimensions. I know Google has it's secret icon converter - http://www.google.com/s2/favicons?domain=http://facebook.com/ but this converts favicons to 16x16 even if they they were originally larger. So basically I need this, minus the shrinking effect. I've also seen this - http://www.controlstyle.com/articles/programming/text/php-favicon/ but I couldn't get it to work after hours of messing around with it. Basically I am trying to automatically grab the icon for a link that will be as large as possible - automatically 48x48 png based on a URL would be the perfect scenario, but I don't know of any humanly possible way to do this given that no websites happen to keep a 48x48 icon in a publicly accessible spot. Does anybody know of a script/service or have a suggestion? Thanks!

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  • how can i make this html page?

    - by From.ME.to.YOU
    hello my HTML code <html> <body> <div id="header">xx</div> <div id="body">yy</div> <div id="footer">zz</div> </body> </html> my problem is with their heights i want it to be like this header :: height 20% body :: height 60% footer :: height 20% is that possible ? thanks

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  • Proxy Error 502 "Reason: Error reading from remote server" with Apache 2.2.3 (Debian) mod_proxy and Jetty 6.1.18

    - by Martin
    Apache is receiving requests at port :80 and proxying them to Jetty at port :8080 The proxy server received an invalid response from an upstream server The proxy server could not handle the request GET /. My dilemma: Everything works fine normally (fast requests, few seconds or few tens of seconds long requests are processed ok). Problems occur when request processing takes long (few minutes?). If I issue request instead directly to Jetty at port :8080 the request is processed OK. So problem is likely to sit somewhere between Apache and Jetty where I am using mod_proxy. How to solve this? I have already tried some "tricks" related to KeepAlive settings, without luck. Here is my current configuration, any suggestions? #keepalive Off ## I have tried this, does not help #SetEnv force-proxy-request-1.0 1 ## I have tried this, does not help #SetEnv proxy-nokeepalive 1 ## I have tried this, does not help #SetEnv proxy-initial-not-pooled 1 ## I have tried this, does not help KeepAlive 20 ## I have tried this, does not help KeepAliveTimeout 600 ## I have tried this, does not help ProxyTimeout 600 ## I have tried this, does not help NameVirtualHost *:80 <VirtualHost _default_:80> ServerAdmin [email protected] ServerName www.mydomain.fi ServerAlias mydomain.fi mydomain.com mydomain www.mydomain.com ProxyRequests On ProxyVia On <Proxy *> Order deny,allow Allow from all </Proxy> ProxyRequests Off ProxyPass / http://www.mydomain.fi:8080/ retry=1 acquire=3000 timeout=600 ProxyPassReverse / http://www.mydomain.fi:8080/ RewriteEngine On RewriteCond %{SERVER_NAME} !^www\.mydomain\.fi RewriteRule /(.*) http://www.mydomain.fi/$1 [redirect=301L] ErrorLog /var/log/apache2/error.log # Possible values include: debug, info, notice, warn, error, crit, # alert, emerg. LogLevel warn CustomLog /var/log/apache2/access.log combined ServerSignature On </VirtualHost> Here is also the debug log from a failing request: 74.125.43.99 - - [29/Sep/2010:20:15:40 +0300] "GET /?wicket:bookmarkablePage=newWindow:com.mydomain.view.application.reports.SaveReportPage HTTP/1.1" 502 355 "https://www.mydomain.fi/?wicket:interface=:0:2:::" "Mozilla/5.0 (Windows; U; Windows NT 6.1; fi; rv:1.9.2.10) Gecko/20100914 Firefox/3.6.10" [Wed Sep 29 20:20:40 2010] [error] [client 74.125.43.99] proxy: error reading status line from remote server www.mydomain.fi, referer: https://www.mydomain.fi/?wicket:interface=:0:2::: [Wed Sep 29 20:20:40 2010] [error] [client 74.125.43.99] proxy: Error reading from remote server returned by /, referer: https://www.mydomain.fi/?wicket:interface=:0:2:::

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  • MaxRequestLen error when i use https

    - by david
    When i got MaxRequestLen errors in file upload page, i set MaxRequestLen=31457280 using: <IfModule mod_fcgid.c> MaxRequestLen 31457280 FcgidIOTimeout 90 </IfModule> Now file upload works when i use http url. I have recently configured ssl for my site and when i use https url for same upload page, i get the same error: HTTP request length 131073 (so far) exceeds MaxRequestLen (131072) Is there a different setting for https? Please help. Thank you.

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  • Trying to figure out URL dispatcher for sluggale URLs like stackoverflow

    - by TylerW
    I'm using the Tornado framework (Python). I have the sluggable URLs working. But I have 3 different entries in the URL dispatcher. I was wondering if someone could help me transform it into one line. This is what I have: (r"/post/([0-9]+)/[a-zA-Z0-9\-]+", SpotHandler), (r"/post/([0-9]+)/", SpotHandler), (r"/post/([0-9]+)", SpotHandler), I want it so that the following URLs all go to the same place. http://domain.com/post/14 http://domain.com/post/14/ http://domain.com/post/14/any-text-it-doesnt-matter-what-it-is

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  • set div position to fixed after scrolling 100px?

    - by user1481850
    I tried to use the following function in order to set the div's position to 100 px from top after scrolling 100 px. <script src="http://code.jquery.com/jquery-latest.js"></script> <script type="text/javascript"> $(window).scroll(function(){ $("#header").css("top",Math.max(0,100-$(this).scrollTop())); }); </script> <div class="header" style="position:fixed;top:100px;background-color:red">something</div> it is not working(the div stick to it's fixed position). it seems that the function is not relating to the div. what is my problem ?

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  • css opacity not working in IE7

    - by Alsciende
    I have this test page : http://jsfiddle.net/VWnm9/7/. The image is correctly faded on all my computers running IE6, 7 or 8, except for one computer that runs IE7 and doesn't fade the flower, even in noext mode. The page is : <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <html lang="en"> <head> <style type="text/css"> body { background: blue; } img { filter: alpha(opacity=10); opacity: 0.1; } </style> </head> <body> <img src="http://upload.wikimedia.org/wikipedia/commons/c/c3/Extracted_pink_rose.png" /> </body> </html> Does anybody have an idea why?

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  • Cannot save properly the source of .html file containing Russian letters as .txt

    - by brilliant
    When I save the source of this page of a Russian website: http://www.mail.ru/ as a .txt file, all Russian letters turn into Chinese characters (I am working on a Chinese computer at the moment), but when I save another page of another Russian website: http://starling.rinet.ru/cgi-bin/response.cgi?root=/usr/local/share/starling/morpho&morpho=0&basename=\usr\local\share\starling\morpho\ozhegov\ozhegov&first=4001 also as a .txt file, all Russian letters are saved in it as the are. Why is it so?

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  • Monitor SOAP 1.2 webservice using OpManager

    - by Tim Mahy
    Hi all, does anyone here know if its possible to monitor using OpManager a SOAP 1.2 webservice and then assert on the result of the request. In the feature list I only see that a Http Get is possible for monitoring websites... what I will need is an Http Post to call the soap webservice... thx in advance, Tim

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  • custom control in DataGridTemplateColumn

    - by Johnsonlu
    Hi all, I'd like to add my custom control into a template column of data grid. The custom control is very similar to a text box, but has an icon in it. The user can click the icon, and selects an item from a prompted window, then the selected item will be filled into the text box. My problem is when the text box is filled, after I click the second column, the text will disappear. If I replace the custom control with a simple text box, the result is the same. Here is the sample code: //Employee.cs using System; using System.Collections.Generic; using System.Linq; using System.Text; namespace SimpleGridTest { public class Employee { public string Department { get; set; } public int ID { get; set; } public string Name { get; set; } } } Mainwindow.xaml <Window x:Class="SimpleGridTest.MainWindow" xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation" xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" Title="MainWindow" Height="350" Width="525"> <Grid> <DataGrid x:Name="grid" Grid.Row="1" Margin="5" AutoGenerateColumns="False" RowHeight="25" RowHeaderWidth="10" ItemsSource="{Binding}" CanUserAddRows="True" CanUserSortColumns="False"> <DataGrid.Columns> <DataGridTemplateColumn Header="Department" Width="150"> <DataGridTemplateColumn.CellTemplate> <DataTemplate> <TextBox Text="{Binding Department}" /> </DataTemplate> </DataGridTemplateColumn.CellTemplate> </DataGridTemplateColumn> <DataGridTextColumn Header="ID" Binding="{Binding Path=ID}" Width="100"/> <DataGridTextColumn Header="Name" Binding="{Binding Path=Name}" Width="200"/> </DataGrid.Columns> </DataGrid> </Grid> </Window> MainWindow.xaml.cs using System.Windows; using System.Collections.ObjectModel; namespace SimpleGridTest { /// <summary> /// Interaction logic for MainWindow.xaml /// </summary> public partial class MainWindow : Window { private ObservableCollection<Employee> _employees = new ObservableCollection<Employee>(); public ObservableCollection<Employee> Employees { get { return _employees; } set { _employees = value; } } public MainWindow() { InitializeComponent(); grid.ItemsSource = Employees; } } } How can I fix this problem? Or I need to write a DataGrid***Column as DataGridTextColumn? Thanks in advance! Best Regards, Johnson

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  • Get a DB result with a value between two column values

    - by vitto
    Hi, I have a database situation where I'd like to get a user profile row by a user age range. this is my db: table_users username age email url pippo 15 [email protected] http://example.com pluto 33 [email protected] http://example.com mikey 78 [email protected] http://example.com table_profiles p_name start_age_range stop_age_range young 10 29 adult 30 69 old 70 inf I use MySQL and PHP but I don't know if there is some specific tacnique to do this and of course if it's possible. # so something like: SELECT * FROM table_profiles AS profiles INNER JOIN table_users AS users # can I do something like this? ON users.age IS BETWEEN profiles.start_age_range AND profiles.stop_age_range

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  • Create a "inset" effect using CSS in websites

    - by Aakash Chakravarthy
    Hello, I am very much impressed by the "inset" like effect in many latest websites. Some examples are and The line in the center. Nowadays, many websites use these kinds of lines/effects. I tried to achieve the same with borders but the color combination is not working me and it is not proper. Do other websites use images for these ? is it easy to this ? Any example css ? Example sites: http://woothemes.com, http://net.tutsplus.com/ , http://www.w3schools.com (in the header) and in wordpress admin page sidebar

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  • I have a question about URI templates in WCF Services

    - by Debby
    I have a web service with following operation contract and my service is hosted at http://localhost:9002/Service.svc/ [OperationContract] [WebGet(UriTemplate = "/Files/{Filepath}")] Stream DownloadFile(string Filepath); This web service would let users download file, if the proper filepath is provided (assuming, I somehow find out that proper filepath). Now, I can access this service from a browser by typing, http://localhost:9002/Service.svc/Files/(Filepath} If {filepath} is some simple string, its not a problem, but I want to send the location of the file. Lets us say users want to download file C:\Test.mp3 on the server. But how can I pass C:\Test.mp3 as {Filepath}? I get an error when I type http://localhost:9002/Service.svc/Files/C:\Test.mp3 in the browser. I am new to web services and find that this community is the quickest way to get answers to my questions.

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  • .htaccess more than one command in the file

    - by Stefan
    Hey I have an .htaccess file with the following code: <Files ~ "item|profile|category|search"> ForceType application/x-httpd-php </Files> What I want is to add a re-write rule as well which changes any body who navigates to the site to use http://www.domain.com sintead of http://domain.com I have the code: RewriteEngine On RewriteCond %{SERVER_PORT} 80 RewriteRule ^(.*)$ http://www.DOMAIN.com/$1 [R,L] however I can't seem to just place in the file as it corrupts? Or just doesn't work... I wish I knew more about .htaccess files How can I add this in? Thanks, Stefan

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  • Issue with Java join() method.

    - by gmunk
    First of all here are some code snippets: http://pastebin.com/9ZCwekXs http://pastebin.com/TtLLXPYP I'm trying to animate some images. The thing is that I want the main thread to wait for the animation thread to finish and then to continue. I searched around, read a little bit and decided to use the join() method. It perfectly waits for the thread to finish but I doesn't animate correctly. The repaint() method gets called 2 times instead of nine. I think maybe the problem is because I used singletons. Here is the singleton implementation. http://pastebin.com/bA3qLZJE

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